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1. 1hvr mvdml Molegro Virtual Docker File Edit View Rendering Preparation Docking Tools Window Help B pl y Q jaw i K E e Hydrogens Fog Hide Residues Search m items Options v Workspace New Backbones 2 O Cavities 1 CO Cofactors 2 a O Constraints 1 F Ligands 1 F Proteins 2 Property Value Selected Atoms 29 Selected Residues 4 Clear Selection 1 1HVR A 1HVR B Figure 26 Sequence viewer with selection of four residues highlighted in the Visualization Window molegro virtual docker user manual 3 User Interface page 37 251 Workspaces can contain user specified notes Further the title of the workspace can be changed using the Workspace Properties dialog The Workspace Properties dialog can be found in the Edit Properties context menu on the Workspace item in the Workspace Explorer or via Edit Workspace Properties see Figure 27 Workspace Properties Workspace title Last saved not set Show properties window when loading workspace User notes Imported notes PDB Header for 1ah3 pdb PDB Header for 2acr pdb Select All Inverse Delete Selected Figure 27 Workspace Properties dialog amens and ANNOTATIONS Distances and angles can be measured directly in the 3D world see Figure 28 If two atoms are selected the distance between them will be shown in the P
2. Open in Pose Organizer Collected results 40 Figure 74 The Multiple Processes Docking Progress Dialog ooe page 105 251 In the Multiple Process Docking Progress Dialog each thread show its current progress While running in multiple process docking mode the main GUI is locked and cannot be used this is in contrast to separate process docking where it is possible to keep using the main GUI After all processes have finished it is possible to open the docking results in the Pose Organizer by pressing the Open in Pose Organizer button There are also other ways to setup multithread docking by running a Molegro Virtual Grid Client and Server on the same machine it is also possible to use multiple cores see Chapter 15 8 Multiple Process Docking can also be invoked from the command line by specifying a mvdscript file and the number of processes and gpu using the syntax ps lt x gt and gpus lt x gt e g mvd test mvdscript ps 2 gpus 2 molegro virtual docker user manual 6 Docking Functionality page 106 251 It is possible to perform screening runs on a Graphics Processor Unit a GPU in Molegro Virtual Docker The advantage of using a GPU is the speed a modern CPU processor such as the Intel Core i7 980 XE may deliver around 200 GFLOPS FLOPS Floating Point Operations per Second of computational power while a modern GPU such as the GeForce GTX 580 may deliver
3. Example docking with different population sizes FOR Spopsize IN 10 20 30 40 50 OPTIMIZER cavity true popsize Spopsize crossoverrate 0 9 LOAD C BENCHMARK 3PTB mvdml RMSD ligand 0 DOCK NEW ENDFOR SET lt VAR gt lt VALUE gt The SET command can be used to set a variable to a given value Variables must start a identifier Example SET PDB 3PTB LOAD C BENCHMARK SPDB mvdml RMSD ligand 0 DOCK molegro virtual docker user manual 29 Appendix XII MolDock SE MolDock SE simplex evolution is an alternative search heuristic which can be used together with either the Mo Dock or Mo Dock Grid scoring functions It is known to perform better on some complexes where the standard MolDock algorithm fails This is usually the case when the ligand has lots of internal degrees of freedom many torsion angles While other algorithms based on parallel simplex search exist our implementation has been modified to be suitable for docking by the inclusion of the pose generation step and the way the initial simplices are created The algorithm works as follows First an initial population of poses is created The initial number of poses is determined by the population size parameter These poses are built incrementally from their rigid root point The pose generator tests a number of different torsions angles rotations and translations
4. LIGHT number on off ambient diffuse specular x y 2 Sets OpenGL light sources FOG LINEAR near far FOG EXP EXP2 exponent Sets OpenGL fog molegro virtual docker user manual 27 Appendix X Console and Macro Commands page 223 251 FOG OFF COLOR protein pose ligand water cofactor fixed cpk i hbond hbond2 interaction For more information about color styles see the interaction2 r g b Visualization Settings dialog section Sets the color style of specified object Sets the visualization style of specified object STYLE protein pose ligand water cofactor vdw fixed stick wireframe none atomScale bondScale lineWidth For more information about graphical styles see the Visualization Settings dialog section The last parameter lineWidth is only used in wireframe mode and is the line width in pixels Determines perspective projection mode Angle is PROJECTION perspective the field of view angle for perspective projection orthogonal angle For more information see the Visualization Settings dialog section BACKGROUNDCOLOR rgb Sets the background color LABELCOLOR r g b Sets the label color CAVITYCOLOR r g b Sets the cavity color Rebuilds all objects in the Visualizer Window This command is necessary to call after the visualization styles or coloring schemes have been updated Otherwise graphical changes will not be reflect
5. OPTIMIZER cavity true popsize 50 scalingfactor 0 50 crossoverrate 0 90 offspringstrategy 1 terminationscheme 0 earlytermination 0 01 clusterthreshold 0 0 LOAD SomeComplex mvdml DOCK When inspecting the docking results in the Pose Organizer it is possible to automatically view the receptor conformation corresponding to the selected pose This is done by enabling Show matching receptor configuration under Settings Dynamic update in the Pose Organizer dialog Notice this requires that the Pose Organizer is in Dynamic Update mode For more information see Section 7 1 molegro virtual docker user manual 9 Displaceable Water Under normal circumstances good docking results may be obtained without taking explicit water molecules into account However sometimes water molecules can play a key role in a protein ligand interactions by forming or mediating hydrogen bonds between the protein and the ligand In such cases taking explicit water into account during docking may be necessary to improve the docking accuracy However even for a protein structure with explicit water molecules the ligand may displace them One way of handling this would be to manually create multiple receptor configurations with individual water molecules toggled on or off In MVD the displaceable water model makes it possible for a ligand to keep favorable and displace non favorable water molecules during docking The identification of key
6. The Value column displays the various terms which the PLANTS Score is based on The PLANTS Score column shows how the PLANTS score energy is composed The PLANTS score is a sum of a subset of the Value terms all terms are given the same weight For the MolDock scoring function the following columns are available The Value column displays the various terms which the MolDock Score and the Rerank Score are based on The MolDock Score column shows how the MolDock score energy is composed The MolDock score is a sum of a subset of the Value terms all terms are given the same weight The Rerank Score uses a weighted combination of the terms used by the MolDock score mixed with a few addition terms the Rerank Score includes the Steric by LJ12 6 terms which are Lennard Jones approximations to the steric energy the MolDock score uses a piecewise linear potential to approximate the steric energy The coefficients for the weighted Rerank Score are given in the Rerank Weight column and the weighted terms and their summations are given in the Rerank Score column The relation between the terms showed in the Ligand Energy Inspector and the terms found in a mvdresults file is shown in the table below Ligand Energy Inspector Term MVDResults Term Total Energy External Ligand interaction Protein Ligand interactions Steric by PLP Steric Steric by LJ12 6 VdW LJ12 6 Hydrogen bonds HBon
7. ssssssnsnrrsronnnnsnsnnnnnnsannnnnnnanrrrennunnrnnnnnnan 37 3 13 Measurements and AnnotationS s ssssssssssssssrrsssnrrrnnsnnrrrrnnnnrrresn 37 3 14 Selection of Atoms Amino Acids Rings and Molecules ccceee 38 3 15 Custom Coloring of Atoms Amino Acids and Molecules 00065 38 3 16 Creating Capel S osivae voters sett atebeecatenedntieaheataesa kanes a a E 39 3 17 Creating Molecular SurfaceS ssssssssssssssnrrssssnnnnresannnnrssannrrnsenens 40 3 18 Creating Protein Backbone ViSUAIIZATIONS 0 ccc eee e eee e ee eeeeees 42 3 19 Making Screenshots t csictcnsestubccersnrseceswia t ewanatexenescaeeuasaumuseseeaees 45 3 20 Sidechain Minimization sssssssssssssssrrrssssnnnrrsnnnnrrrnnnnrrrennnrrssesnnas 45 3 21 Working With Multiple Receptor ConformationS ssssssrrsrrsrrsrrene 48 3 22 Visualization Settings Dialog sssssssssssssassrrssrrrsrrnnrinnrinsrrrsrrnnnas 50 3 23 High Quality Rendering ssssssssssssrsnsrrrsrrrsrrrnrrnnrinenrrnrrrsrrrnnrenn 56 3 24 Biomolecule Generator eeu sessadececedecuswednaavsedinswnccouswiddeniuecdauieceseesde 58 3 25 Structural Alignment of ProveiiSs s csisavcecopennverecesenaenedpesasensddandsenres 60 3 26 Structural Alignment of Small Molecules cccccccseeeeeeeeeeeeeeeeanes 61 3 27 Macro and Menu EditO esiscscesivescevistscasavid roinaa 61 3 28 PDB and SDF Import NoteS ssssssssssssrrrrsssrrrrsrsrrrrrrerrrrresnnrrrenns 63 Sie 9 Ener
8. Ensures that we use the built in algorithm to determine atom connectivity PREPARE Charges IfMissing Uses the charges from the molecular input file default is to overwrite them LOAD lt mvdmIi filename gt Loads a workspace from a MVDML file Notice that this command will replace the current workspace No preparation is done on the workspace since it is assumed that files saved in MVDML format are prepared already Notice LOAD clears the current workspace if any SAVE lt mvdml filename gt Save the current workspace as a MVDML file All molecular structures in the workspace are saved molegro virtual docker user manual 28 Appendix XI Script Commands page 229 251 EXIT Causes the MVD process to terminate This can be useful if running several docking simulations of different proteins automated from a scripting language i e using the Python wrapper Do not use this command when parsing a text file script as it will terminate the script and not parse anything after the EXIT command DOCK lt molecules gt The DOCK command initiates the docking process lt molecules gt is a list of ligands notice only ligands are allowed here to be docked lt molecules gt is specified in the usual target format The settings for the docking can be modified using the DOCKSETTINGS command The docking scoring function and search algorithm can be mo
9. V Hydrogen positions are optimized Optimize ligand and protein hydrogen positions using the Action menu before enabling this option Re evaluate Copy tables to clipboard Figure 82 Settings tab page for MolDock Score The last option relates to hydrogen bond evaluation When estimating hydrogen bonds MVD does not automatically assume that rotatable hydrogen bond donors have their hydrogen atoms positioned correctly However if the hydrogen positions have been optimized using Action Optimize Ligand and Protein Hydrogen Positions enable this option to take the full geometry of the hydrogen bond into account For the PLANTS Score the following options are available Include hydrogens in torsion term toggles whether or not hydrogens should be included when calculating the Tripos torsion potential see Appendix II PLANTS Scoring Function for details about the PLANTS scoring function The Use original Plants setup option toggles between original Plants setup using PLANTS specific binding penalty terms and ignoring entries with dummy Tripos atom types in Tripos torsion potential and MVD molegro virtual docker user manual 7 Analyzing the Docking Results page 127 251 implementation of PLANTS score using another binding penalty term and including dummy Tripos atom types in Tripos torsion potential See Appendix II PLANTS Scoring Function for details about the different binding penalty terms available
10. When two proteins have been chosen the list on the right side of the dialog will suggest a matching between residues in the proteins Green entries indicate which residues that will be aligned By default the matching will be done using Match by residue type and PDB index where two residues will molegro virtual docker user manual 3 User Interface page 61 251 be matched if they are of the same kind and have identical PDB residue identifiers Two PDB crystal structures may have similar sequences but different PDB residue identifiers In this case it is possible to Match by residue type and position This will match two residues if their positions in the sequences are identical It is also possible to add a index offset to the target protein index Sometimes a number of other molecules are associated with a protein a bound ligand or cofactor or another protein chain It is possible to select a number of additional molecules and apply the same transformation that aligns the target protein to the reference protein to the additional molecules This is done by checking the desired molecules in the workspace view on the left side of the dialog Notice that if the reference or target protein is selected as part of an additional alignment they will be ignored since they are already considered Simple alignment of small molecules is also possible By selecting three atoms in one ligand and selecting three atoms in another ligand a ne
11. 10 Cumi cule E E iy Only selected atoms E Proteins 2 2 O Ligands 0 5 Figure 29 Creating a new label The Create Label dialog makes it possible to label different object levels atoms bonds molecules or residues The labels can be chosen from a list of molegro virtual docker user manual 3 User Interface page 40 251 standard templates or constructed from a list of available variables using the Advanced tab Create Label Label Type Template Residue name and chain ID Target s F Only residues with at least one selected atom Label Expression Proteins 2 2 NAME CHAINT Enter labe expression in the combobox above Variable names will be substituted when evaluated Variables can be inserted from the list below Variables CHAIN Chain Name CHAINT Truncated Chain Name ID Intemal Index UCTTCO 1l ntter leone Figure 30 Advanced label expression dialog Labels will occur in the Labels category in the Workspace Explorer assigned in groups one group for each molecule Labels can be removed or hidden using the context menu or by pressing the labels tool bar button Surfaces can be created for all molecular objects via Create Surface from the context menu in the Workspace Explorer or via Tools Surfaces In MVD surfaces are created by probing points on a uniformly spaced grid It is possible to adjust the grid resolution Resolution
12. If you want to import MVDML files use the LOAD command If a complete file path is not specified the current working directory is used to search for the files see the CD command The importer is able to read UTF 8 or UTF 16 Unicode encoded files It is also able to read 8 bit Local encoded files but will not parse special national characters correctly If errors are encountered with special characters for instance in the name of the ligands try converting the files to Unicode IM PO RT Ligand 1 3 FROM testdock mol2 PO All FROM testdock mol2 PO l Proteins Waters Cofactors FROM lhvr pdb molegro virtual docker user manual 28 Appendix XI Script Commands page 228 251 PREPARE lt settings string gt Determines how molecules imported using the IMPORT command are prepared The settings string is composed of semi colon separated pairs of a preparation type and its preparation scheme Preparation Types Bonds BondOrders Hydrogens Charges or TorsionTrees Preparation Schemes IfMissing Always Never or Remove The default setting is PREPARE Bonds IfMissing BondOrders IfMissing Hydrogens IfMissing Charges Always TorsionTrees Always It is not necessary to specify all of the PREPARE settings If only some of them are specified the default parameters will be used for the remainder Examples PREPARE Bonds Always
13. MVD script file MVD script log file docking results file and found poses will be stored The MVD script file script mvdscript contains the scripting commands automatically generated to perform the docking simulation The MVD script log file ScriptLog timestamp txt is a time stamped log file containing log information generated by the script interpreter Details about the poses returned after the docking simulation e g docking score affinity specific energy terms and pose Mol2 filename are included in a mvdresults file DockingResults mvdresults The mvdresults file is used by the Pose Organizer to show detailed information about the poses and to dynamically load the molecular structure of the poses see Section 7 1 for more details Each pose is stored in either Mol2 or MVDML format as chosen in the Save found poses as combobox The poses are used by the Pose Organizer to show the 3D conformations of the poses in the Visualization Window The Pose name pattern specifies how the poses should be named when saved By default ID Name is used but the pattern can be changed if white spaces or square brackets should be omitted from the pose filename If the Create SMILES in MVDResults file is enabled a column with SMILES strings is added to the MVDResults output This makes it possible to visualize 2D depictions of the molecules in Molegro Data Modeller when analyzing docking data molegro virtual docker user manual 6
14. Max iterations default 1500 The number of steps per run These steps are evenly divided between the pose generator and the simplex evolution algorithm even though both of these may terminate before the number of iterations has been used Max population size default 50 The number of individuals in the simplex evolution phase Notice that this number must be higher than the number of degrees of freedom 7 spatial degrees of freedom plus the number of chosen rotatable torsion bonds Energy threshold default 100 00 Poses are only added to the population if the value is below this threshold Notice that when half of the iterations in the docking run have been used this threshold is automatically turned off in order to ensure that enough poses are created for the simplex evolution phase Tries Min Quick Max At each step at least min torsions translations rotations are tested and the one giving lowest energy is chosen If the energy is positive i e because of a clash or an unfavorable electrostatic interaction then additional max positions will be tested If it is not possible to construct a component which do not clash the max tries number is lowered to the quick try value Max Steps default 300 The number of iterations of the Nelder Mead molegro virtual docker user manual 29 Appendix XII MolDock SE page 245 251 simplex minimization procedure performed at each step of the MolDock SE algorithm Neighbo
15. Proteins 3PTB A Cofactors Wi CA_480 A Structural Water Wi All waters From extemal data source File C Users Molegro Desktop Molecules s 100 sdf Index 3 From KNIME workflow Reference ligand for RMSD calculations None lt Back Figure 59 Using data sources from the Docking Wizard molegro virtual docker user manual 5 Data Sources page 84 251 When choosing Setup a dialog for defining the data source appears S Data Source Data source Preparation Specify the data source Examples File Molecules sdf Index 10 100 10000 10010 Dir G Molecules pattem sdf mol2 Index 40 1000 Data source description File C Users Molegro Desktop Molecules s 100 sdf Index 3 Figure 60 Specifying a data source Specify the data source on the Data source description line input or use either the Dir or File button to choose a directory or file from a dialog The Preparation tab determines how the data source should be prepared These settings are described in Section 4 2 Loading Data Sources Directly into the Workspace By using the File Import From Datasource menu item it is possible to directly load a number of molecules into the workspace This can be useful for importing a small subset of the molecules in a data source to check that the parsing and preparation is okay Notice that all molecules are loaded into memory which can m
16. and probe size Probe Radius under Advanced settings Two types of surfaces are available Expanded Van der Waals this is an approximation to the surface created by expanding the Van der Waals radius of each atom with the Probe Radius Molecular surface this is an approximation to the surface defined by the contact area of the probe and Van der Waals sized spheres molegro virtual docker user manual 3 User Interface page 41 251 It is also possible to restrict the surface to a volume defined by the current search space by enabling Restrict to search space Surfaces can be colored by Hydrophobicity Electrostatic Potential or Solid Color Surfaces can be drawn transparently as dots lines or solid polygons Surface Target Appearance Advanced gt gt gt Surface type coloring Electrostatic eee acan Figure 31 Creating a new surface molegro virtual docker user manual 3 User Interface page 42 251 Solid Transparency F oowoo Figure 32 Changing surface appearance 3 18 Creating Protein Backbone Visualizations The backbone of the protein can be visualized by using the Create Backbone Visualization dialog The dialog can be invoked by using the context menu on the Proteins category or a single protein item in the Workspace Explorer Color interpolation 7 Diameter A 0 30 Subdivisions 8 E Proteins 2 2 a v
17. assigns a penalty of 1000 if the distance between two heavy atoms more than two bonds apart is less than 2 0 A Thus Eaasn term punishes infeasible ligand conformations Finally if a ligand heavy atom is located outside the binding site region defined by the search space sphere a constant penalty of 10000 is assigned to the total energy notice this penalty scheme is only used for the grid based version of the MolDock Score Bo mA sp sp gt 0 0 6 1 5 sp sp gt s T 3 3 0 sp sp 0 2 3 0 Table 6 Torsional parameters the sp sp term is not enabled by default After MVD has predicted one or more promising poses using the MolDock score it calculates several additional energy terms All of these terms are stored in the DockingResults mvdresults file at the end of the docking run The rerank score is a linear combination of these terms weighted by the coefficients given in the RerankingCoefficients txt A mvdresults file is not meant to be interpreted or inspected manually Instead it should be opened in MVD either by dragging it onto the workspace or by selecting File Import Docking Results mvdresults It is also possible to open the file in Molegro Data Modeller in order to create new regression models based on the energy terms in the file The following table explains the different terms in a mvdresults file Textual Information Ligand The name of the ligand th
18. chain ID option is used to decide whether or not molecule fragments should be combined during import Molecule fragments can be combined if any atom in one fragment can form a covalent bond to any other atom in another fragment Molecule fragments can only be combined if they share either Mol2 substructure IDs or chain IDs in the case of PDB files When the Use hybridization from Sybyl atom types option is enabled Sybyl atom types will be used to determine hybridization if they are available during import Otherwise the default geometric heuristic is used see Appendix VII Automatic Preparation for details The final option SDF data header for molecule names SDF files only can be used to specify the name of the SDF data header that will be used for naming molecules during import instead of using the first line in each molecule header The first line will also be used if the file does not contain the specified data header The preference settings are stored when exiting the MVD application The location of the saved settings depends on the operating system used a Windows the settings are stored in the system registry a Mac OS X the settings are stored in a com molegro MVD plist file located in the lt user folder gt Library Preferences folder m Linux the settings are stored in a mvdrc file located in a hidden folder named lt user folder gt molegro Currently the following command line parameters are availa
19. evaporationrate double 0 15 Evaporation rate used to adjust pheromone trails see KORB 2009 for details iterationsdbupdate int 5 If the best found solution in the last iterationsdbupdate number of iterations has higher energy score than the the best solution found since the last diversification event diversification solution the diversification solution is used to update the pheromone trails see KORB 2009 for details This setting requires that diversify true iterationsgbterminate int 1 The algorithm is terminated if the global molegro virtual docker user manual 28 Appendix XI Script Commands page 235 251 OPTIMIZER lt initstring gt best found solution has not been improved for the last iterationsgbterminate number of iterations The best found solution found is returned The default settings using the MolDock search algorithm from the Docking Wizard will generate the following optimizer string OPTIMIZER cavity false popsize 50 scalingfactor 0 50 crossoverrate 0 90 offspringstrategy 1 terminationscheme 0 earlytermination 0 01 clusterthreshold 1 00 keepmaxposes 5 Another example using the MolDock SE search algorithm OPTIMIZER populationsize 50 cavity true creationenergythreshold 100 posegenerator 10 10 30 maxsimplex 750 simplexsteps 300 simplexdistancefactor l Notice an easy way to generate a Suitable initstring is to use the Docking Wizard to
20. fa st Ligand Energy Inspector Ligand pose E Hide other ligands poses Action v Ligand Targets Total Energy Displaceable Water Settings Water Energies Options v ID Type lt Energy contribution Energy waterligand Ener 5 Non displaced 0 124031 0 124031 18 76 Non displaced 4 06245 4 06245 Non displaced 0 774477 0 774477 Non displaced 0 000339798 0 000339798 Non displaced 1 62253 1 62253 ignored 0 0 ignored ignored ignored ignored fignored ignored ignored ignored ignored ignored fianored OoOoooo0o o 0000 amp gooqeooeooocococ amp Copy tables to clipboard Figure 93 Displaceable Water tab Listing of non displaced displaced and ignored water molecules Displacable Water interactions is also shown in the Energy Total tab see Figure 94 molegro virtual docker user manual 9 Displaceable Water page 146 251 Ligand Energy Inspector Ligand pose BEN_1 A E Hide other ligands poses Ligand Targets Total Energy Displaceable Water Descriptors Value E Total Energy Extemal Ligand interactions Protein Ligand interactions Steric by PLP Steric by LJ12 6 Hydrogen bonds Hydrogen bonds no directionality Electrostatic short range Electrostatic long range Cofactor Ligand Steric by PLP Steric by LJ12 6 Hydrogen bonds Electrostatic B Intemal Ligand interactions Torsio
21. if the template was constructed from one ligand only this ligand would have a normalized template score of 1 0 Notice that in the docking wizard it is possible to specify an overall normalization of the similarity score term to molegro virtual docker user manual 10 Template Docking page 150 251 balance it with other scoring terms the default overall normalization when docking is 500 0 ANY Catting n Tamnrnlatna Darling 10 2 Setting up Template Dockin In order to setup template docking import the desired reference ligands into the workspace and select Docking Setup template docking gL Template Docking Wizard Choose Ligands Similarity Measure Select one or more ligands and press Create template Poses similar to the templates are rewarded during the docking BEN_1 A 18 atoms Merge atoms closer than A Charge threshold b T Only selected atoms Cancel Figure 97 The Template Docking Wizard On the first tab in the template wizard the reference ligands are specified When pressing the Create Template button the docking template is created If only one ligand is selected the procedure is straight forward each atom in the chosen ligand is tested against the predefined template groups and if the atoms match the position of the atom is added to the group as a new group center Notice that only heavy atoms are taken into account when creating the template hydrogen
22. licensedir parameter can be used to specify another directory where the MVD license is located By default MVD checks for the license file in the same directory as the MVD executable e g Molegro MVD bin Example Molegro MVD bin mvd licensedir Molegro License Finally the macro lt label gt parameter can be used to specify a macro that is executed when starting up MVD This can be useful for e g setting up a user customized visualization style when running MVD The macro label is used to identify which macro to execute the labels can be added or modified in the Macro and Menu Editor dialog Notice that labels are not allowed to contain white spaces Example Molegro MVD bin mvd macro MyOwnMacro The energy terms and their weights coefficients used in the reranking scoring function can be altered by modifying the RerankingCoefficients txt file located inthe Misc Data directory located within the main directory of MVD Notice Changing these coefficients and disabling enabling energy terms will alter the performance of the reranking score used in the Pose Organizer dialog and may result in much worse performance Remember to backup the original file before modifying the coefficients molegro virtual docker user manual 12 Obtaining the Best Docking Results This section takes a closer look at the most important aspects regarding preparation docking and post analysis that can be decisive for whether
23. set during preparation Molecules can be manually prepared using the context menus of highlighted atoms or bonds see below Hybridization SP SP2 SP3 can be manually assigned to atoms by right clicking on the atom in question and selecting the Set Hybridization menu option The hydrogen bond type used by MolDock scoring function donor acceptor both non polar can be manually assigned to atoms by right clicking on the atom in question and selecting the Set Hydrogen Bond Type menu option Sometimes the built in assignment scheme fails in assigning correct Tripos atom types to specific atom In such cases it is possible to change the Tripos atom type for nitrogen oxygen carbon and sulphur atoms by right clicking on the atom in question and selecting the Set Tripos Atom Type menu option By default MVD automatically assigns Plants atom types Donor Acceptor molegro virtual docker user manual 4 Preparation page 72 251 Both Nonpolar Metal before docking with PLANTS Score using the rules described in KORB 2009 However it is also possible to manually assign the Plants atom type by right clicking on the atom in question and selecting the Set Plants Atom Type menu option Notice Plants atom types are not defined for hydrogen atoms The Set Hydrogen Count menu option can be used to set the number of explicit hydrogens attached to the highlighted atom The MolDock scoring function uses partial charges assigned wh
24. 1 6 Screenshots Used In the Manual ccccscseeeeeeesssseeeeeeeeeennnsneenens 9 1 7 Me CO AOC S eiatsccucads aavaes steer sven seteuncee aan e seen san aenn aenennsassateueenee 9 2 DOCKING MGCOMAlbcocuscaenstscunncincssamuccaaieesetascnceeseesadesmsnaceencn erase ERAEN 11 2 1 Importing and Preparing MOI CUIES cccecceeeseeeeeneeeeeeneeerensaeeees 11 2 2 Running the Docking Simulation ccccccceesseeeeeeeeeeeeeeeeensseeeeaaaees 17 2 3 Viewing the RESUITS sccivctssciiecsawsacde cia iocaecasovanhscasewisesdeeiecsdecsseiensaces 22 3 User INES ACCs 4 scscccnecpactenssaccancenetasnsannewincuansesteameeucteunseasenacoosestescanee 24 Suk Basic CONCEDLS rriren aa a E a 24 3 2 TIVE VICW esensi erivisisobriorsyi iere eresi ere i e aa eee Ea eiei 24 3 3 NOGID AP ariran on ea EAEE EA aa 25 3 4 Workspace EX plo lel exciidecesvcarcssuadecdsunatddecnsretecketineerssciesneseesselaguese 26 3 5 Properties WINDOW 2 ccc c2cesaceexeecenapditndeasetbenserciaeccserasanuentaniontestoseares 28 3 0 CONSOIS WINdOW rici i n a EE E E eee E a 31 3 7 Clipping Plane Senispnisinipcennonee nn n in eine 32 3 8 Creating a Search SpaCe sssssssssrrrresannrrrssannrrssernnnsnsnnnesssnnnreenn 32 3 9 Hiding Distant ResidueS sssssssssssssssrrrsrrrerrrnsrnnrrnrrrrerrrenrrssrennas 33 3 10 Wo rkspace Finde iiss conccastosugunsteumensestnasennesds ARA REE AR AE 34 3 11 SEQUENCE VIEWER misne r aE EEEE PE E EAE EEE EEA 35 3 12 Workspace PropertieS
25. 166 251 However for large proteins or proteins having a lot of cavities it is sometimes necessary to increase the number of cavities reported Max number of cavities Also remember to set the binding site Origin in the Docking Wizard to the specific cavity being investigated a Domain knowledge The success of the docking run can be significantly improved if any domain knowledge is available For instance knowledge about preferred binding mode or ligand conformation can be used to set constraints or reduce the search space covered e g constraints and binding site settings in the Docking Wizard a In some cases docking performance can be improved by selecting another ligand root atom right click on ligand atom and select Set as Root Atom The current root atom can be visually identified if visualization of root atoms is enabled see Section 11 1 The root atom is used as root in the torsion tree that is constructed when docking flexible ligands Docking performance may be improved by setting the root atom in a region of the ligand that is suspected to contribute significantly to the docking energy ms Size of search space The size and location of the volume that the docking search algorithm will sample is defined by the Binding site settings in the Docking Wizard Before starting the docking run potential cavities should be identified see Section 6 1 Found cavities can be used to specify the origin of the search space in the Doc
26. 7 Sp2 Sp2 Torsions Displaceable Water Entropy reward for each water displaced 0 00 A Figure 65 Choosing scoring function For the PLANTS Score the following options are available Include hydrogens in torsion term toggles whether or not hydrogens should be included when calculating the Tripos torsion potential see Appendix II PLANTS Scoring Function for details about the PLANTS scoring function The Ignore distant atoms option is used to ignore atoms some distance away from the binding site and is similar to the option for the MolDock score If water molecules are available in the workspace it is possible to include molegro virtual docker user manual 6 Docking Functionality page 94 251 displaceable water evaluation by enabling the Displaceable Water option see Section 9 1 for more details For the grid based scoring functions the Grid resolution option not shown in Figure 65 can be used to set the granularity of the generated energy grids The Binding site specifies the region of interest and thus where the docking procedure will look for promising poses ligand conformations The Origin determines which area of the protein is expected to include the binding site If cavities have been identified the user can pick one of these as the preferred area of interest Further if a reference ligand is being used the center of the reference ligand can be used By default if no cavities have been identified
27. Docking Functionality page 102 251 Docking W zard Setup Docking Execution Choose how to execute the docking Run docking in separate process Greates a scapt and executes if in an extemal process You can continue working on the current workspace Run docking in multiple processes Oe ee ee ee a CPU Processes 1 GPU s 0 Create a docking scriptjob but do not run it now Can be used to prepare larger docking runs e g on several machines Start job on Virtual Grid Virtual Grid docking is only enabled when docking from a data source Edit script manually Data output Output directory C Users Molegro Documents MVD Data DockingOutpi an Save found poses as MVDML MVD XML format x Pose name pattem SID SNAME e g 01 molecule mvdml V Create SMILES in MVDResults file The generated script the logfile and the found poses will be stored in the output directory rrem Figure 71 Setup docking execution Finally when the Start button is pressed the docking run will start and the Molegro Virtual Docker Batchjob dialog will pop up showing the current status and progress of the docking see Figures 72 and 73 molegro virtual docker user manual 6 Docking Functionality Molegro Virtual Docker Batchjob Running Batchjob started ma 27 aug 10 11 51 2012 Elapsed 00 00 11 Finish estimated 10 13 34 Remaining 00 01 32 Working path C Users Mikael Documents
28. Docking progress 0 Oligands 0 Current ligand 0 0 runs 0 Log Poses curent ligand Poses all Graph Current script Time It iw Ve ae Bong meen Se Vp 14 15 35 072 Creating MolDock SE instance 14 15 35 074 With the following evaluator MolegroGridEvaluator 14 15 35 075 Setting optimizer init string populationsize 50 cavity true creation Energy Threshold 100 poseGenera 14 15 35 078 The random seed used for this session is 3712317356 14 15 35 079 Optimizer MolDock SE params populationsize 50 randomizeligand 1 cavity 1 recombine 1 crea 14 15 35 081 Evaluator Grid Resolution 0 3 Torsion scheme 1 Damp factor 1 Include ligand electrostatics No 14 15 35 082 Creating Docking Results file C Users Mikael Documents MVD Data DockingOutput 232 Dockin 14 15 35 119 Notice MolegroGridEvaluator ignores cropdistance argument 14 15 35 121 Notice MolegroGridEvaluator ignores hbond90 argument 14 15 35 182 Docking ligand XK2_263 14 15 35 183 Beginning run 1 out of 10 14 15 35 185 Source Ligand was randomized This will destroy its original orientation 14 15 35 186 Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVD Visual Studio Release 14 15 35 218 Reading 626 values 14 15 35 219 Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStudio Release Status Finished Pause Figure 121 Script Progress GUI
29. MVD includes three search algorithms for molecular docking Mo Dock Optimizer THOMSEN 2006 Mo Dock SE simplex evolution and Iterated Simplex The Number of runs specifies the number of times that the docking simulation is repeated for each ligand chosen to be docked Sometimes more than one run is needed to identify promising poses in particular for ligands having more than 15 flexible torsions or if no promising cavities exist If cavities have been identified see Section 6 1 the poses found by the search molegro virtual docker user manual 6 Docking Functionality page 96 251 algorithm can be constrained to the region spanned by the cavity by using the Constrain poses to cavity option This option greatly reduces the overall docking process and increases the accuracy of the docking procedure However if the ligand does not bind in the region specified by the selected cavity this option should be disabled The After Docking settings make it possible to perform two post docking steps Energy Minimization performs a short Nelder Mead Simplex minimization of the translation orientation and flexible dihedral angles of the found poses using the MolDock scoring function This step can be used to slightly refine the docking results the evaluation is always performed with a non grid version of the MolDock scoring function thus preventing any inaccuracies due to energy grid approximations Also the non grid MolDock scoring functio
30. More precisely for each given sidechain a sphere bounding all possible configurations of the sidechain is calculated and it is tested whether any atom in the active ligand is close enough to make a steric contact with an atom in this bounding sphere for the MolDock potential all steric contacts are cut off at a distance of 6 0 A Notice that the Active ligand can be set in the Workspace Explorer window it is the ligand which name is prepended with an Active label Add Visible This will add all sidechains which are currently visible in the 3D Visualization window This feature can be used together with the Hide Residues dialog where it is possible to hide sidechains depending on the distance from some given object Add Selected This feature allows for selecting sidechains directly in the 3D Visualization window A sidechain is selected if one or more atoms inside it are chosen Clear List Removes all sidechains from the list Remove Selected Removes all sidechains that are currently highlighted in the sidechain list view molegro virtual docker user manual 3 User Interface page 47 251 Remove Non selected Removes all sidechains that are not highlighted in the sidechain list view The following columns display information about the selected sidechains Residue The residue name id Protein ID The protein or protein chain ID and name Torsions The number of degrees of freedom in the given sidec
31. REACTIVE SITE AND OF THE PEPTIDE GROUPS TITLE 2 IN TRYPSIN TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS COMPND MOL_ID 1 COMPND 2 MOLECULE BETA TRYPSIN COMPND 3 CHAIN A COMPND 4 EC 3 4 21 4 COMPND S ENGINEERED YES SOURCE MOL_ID 1 SOURCE 2 ORGANISM SCIENTIFIC BOS TAURUS SOURCE 3 ORGANISM COMMON CATTLE SOURCE 4 ORGANISM_TAXID 9913 KEYWDS HYDROLASE SERINE PROTEINASE EXPDTA X RAY DIFFRACTION AUTHOR W BODE P SCHWAGER J WALTER REVDAT 6 24 FEB 09 3PTB 1 VERSN REVDAT 5 14 MAR 85 3PTB 3 SEQRES ATOM REVDAT 4 23 FEB 84 3PTB 1 JRNL REVDAT 3 27 OCT 83 3PTB 1 SPRSDE Figure 50 PDB header information shown for imported PDB file molegro virtual docker user manual 3 User Interface page 64 251 A workspace may contain an arbitrary number of import notes and each molecule may have a reference to one of these notes Imported notes are stored in the MVDML workspace file and they can be viewed and deleted using the Workspace Properties dialog Workspace title Last saved mandag august 27 12 10 12 41 E Show properties window when loading workspace User notes Imported notes PDB Header for 3ptb_1 pdb Select All Inverse Delete Selected Figure 51 Imported PDB and SDF notes can be shown and deleted using the Workspace Properties dialog Notes that are no longer referenced by a molecule are automatically removed 3 29 Energy Maps It is possible to visualize the
32. a energy contribution of 500 Use energy grids toggles whether grids with precalculated energy contributions should be used during the docking It is recommended to use energy grids molegro virtual docker user manual 10 Template Docking page 155 251 Choose Scoring Function and Define Binding Site Scoring function Score Ligand Evaluator Steric interactions Torsional interactions Ligand evaluation E Intemal ES F Intemal HBond F Sp2 Sp2 Torsions Binding site Origin User defined Center X 32 03 3 x 13 46 Radius 15 fel Figure 102 The Ligand Evaluator scoring function When a similarity definition is present in the workspace a new score function appears in the Docking Wizard the Ligand Evaluator The Ligand Evaluator estimates the internal energy of a ligand and is identical to the Entra term in Appendix I MolDock Scoring Function It is possible to enable or disable steric torsional and electrostatic interactions When aligning molecules it is necessary to use the Ligand Evaluator to prevent internal collapse of the ligands otherwise different atoms in the ligands might try to overlap each other in order to satisfy the same template group center Notice that when docking against a protein target combined with a template the Ligand Evaluator should not be used choose a MolDockScore evaluator instead The internal ligand energy terms in the MolDockScore will prevent the l
33. a folder named InputFiles The InputFiles folder must be located in the same folder as the grid job file Notice that the InputFiles cannot contain sub folders all molecule files must be located at the root of the InputFiles folder When the job file is executed by the controller two additional directories are molegro virtual docker user manual 15 Molegro Virtual Grid page 190 251 created The JobState directory contains one file per job unit The extension of the file shows the current state of the job unit e g Unit1 Pending is a job unit waiting for execution and Unit47 DoneAndCollected is a job unit which has completed and the results have been transferred from the agent back to the controller The content of these files is the log file including any log messages produced by MVD during the docking run The OutputFiles directory contains the files that have been transferred from the different agents and back to the controller This includes the molecular structure files the poses and the MVD docking results molegro virtual docker user manual 16 Help 16 1 PDF Help The documentation for Molegro Virtual Docker is available as a PDF file In order to invoke the PDF help using the built in PDF reader choose Help Molegro Virtual Docker Manual from the menu bar The executable for the PDF reader can be specified in the Preferences 16 2 Tip of the Day A Tip of the Day dialog see Figure
34. a location use the Save button to make the setting persistent The agent also requires some space for temporary files files received from the controller or docking result files Specify a directory as above After the MVD path and working directory has been specified the agent is ready to receive jobs It can be minimized to the system tray by pressing the button in the lower right corner The icon both the application icon and the system tray icon will show the number of job units being executed If any errors or warnings are encountered a notification message will be shown from the tray icon Notice that the Growl notification system http growl info must be installed for this to work on Mac OS X molegro virtual docker user manual 15 Molegro Virtual Grid page 183 251 Virtual Grid Agent 3 new warning s aos O Be 139 Figure 117 Example of an Agent running in the task tray on Windows Vista The red icon indicates that an error has occurred The number shows the number of executing job units The green icon is the controller icon The Units list view shows the job units currently being executed in green job units that are pending execution white and job units that are completed but not collected from the controller yet grey Completed job units will be removed from the list when the controller has collected the results Per default the agent starts up as a graphical application but it
35. algorithm Algorithm GPU Screening CUDA Number of runs 10 Constrain poses to cavity no cavities found After docking Energy Minimization V Optimize H Bonds Parameter settings Max iterations 1500 Simultaneous evaluations 256 Re evaluate using CPU scoring function choosen on previous page GPU screening uses an intemal GPU scoring function if Energy Minimization or Optimize H Bonds is enabled poses will be re evaluated using the CPU MolDock Score Notice that Energy Minimization is done using the CPU and slows the screening Altematively the re evaluation option above can be enabled Figure 75 Customizing settings for GPU based screening molegro virtual docker user manual 6 Docking Functionality page 108 251 It is important to notice that in contrast to the other search algorithms the GPU screening algorithm does not use the scoring function specified on the scoring function tab Instead it uses a PlantsPLP like scoring function during the docking search It is however possible to apply a CPU scoring function as specified from the scoring function tab after the docking to rerank the results This can be enabled by checking the Re evaluate using CPU scoring function chosen on previous page The parameters for a GPU Screening are described in the next section The GPU Screening algorithm uses a parallel implementation of the Nelder Mead search algorithm to search the c
36. and aligning the N C and CA backbone atoms with the N C and CA backbone atoms for the chosen residue After having substituted the new residue it is recommended to optimize its position A quick optimization can be performed by choosing Optimize Residue This will perform a search for the best dihedral angles for the residue It is also possible to optimize the positions of neighbouring residues as well The optimization uses the same approach as the Sidechain Minimization dialog which is described in Section 3 20 By choosing Optimize Neighbours both the chosen residue and the residues which are closest to it are selected The selection is done as follows each residue is assigned a bounding sphere a sphere which is large enough to enclose the residue in all possible conformations If the distance between two residues are less than the threshold distance specified in the settings tab Residue neighbour distance A the residues are considered to be neighbours By default the neighbour distance is 0 A meaning that the bounding spheres must overlap for residues to be considered neighbours Increasing the distance results in a larger neighbourhood molegro virtual docker user manual 4 Preparation page 77 251 The following settings can be customized Check and correct charges If this option is checked all atomic partial charges are validated against the values defined in the protonation template file The charges defined in thi
37. at a time It is possible to use any number of cores on this single machine but only one physical machine can be used at a time This machine can either be the same machine as Molegro Virtual Docker and the MVG controller is running on this is useful in order to take advantage of the multiple cores or another machine for instance the MVD GUI can be run on a laptop while the docking runs are executed on a more powerful desktop computer The extended license which is licensed as an additional product has no restrictions on the number of machines it controls Together with the features in the MVG controller for combining and filtering docking results it is possible to run very large docking runs In order for a machine to participate in the grid and receive job units it must run the Molegro Virtual Grid Agent and have copy of Molegro Virtual Docker together with a valid license installed In order to start an agent on a machine run the Virtual Grid executable On Windows this file is called virtualgrid exe and is located in the bin directory of the Molegro Virtual Docker installation On Linux and Mac the file is called virtualgrid The agent writes a log file to its working directory while running The filename for this log file is auto generated A typical filename will be Log 24 11 2009 16 27 28 153 txt The log file is useful for detecting docking run errors and configuration errors The log file can also be retrieved usi
38. atoms are simply ignored If Only selected atoms is checked only the atoms that have been selected in the 3D view are taken into account this can be useful for creating a template from a subset of a ligand If several ligands are chosen MVD first creates a docking template from the first ligand as above Then each atom from the remaining ligands are compared to the existing centers from the template being constructed If an atom is closer to an existing center than the threshold specified in the wizard default 1 2 the atom will be considered equal to that center Notice that a molegro virtual docker user manual 10 Template Docking page 151 251 center can be part of several template groups if any of the existing groups that the center is part of do not match the atom the center is removed from them the center is degraded in order to match both the current atom and the atom which defined the original group The Charge threshold option is used to specify a charge threshold default 0 2 for positive and negative charges Atoms with a numerical charge less than this threshold are not considered charged S Template Docking Wizard Choose Ligands Similarity Measure Setup Similarity Groups Group Radius Strength Count 1 1 1 1 Charge threshold 0 Z Enabled Radius A 1 80 Strength 1 00 Figure 98 Customizing the similarity measure By choosing the Similarity Measure
39. been interpreted A small Python wrapper is provided in MVD Scripting Python MvdWrapper py The wrapper encapsulates the various script commands in a small object MVDWrapper The wrapper spawns a new MVD process when the object is instantiated and runs MVD in interactive mode to pass commands to it The process can be terminated by calling exit on it In order to use the wrapper copy the MvdWrapper py file to the same location as your Python script or install it in a globally accessible location and import it at the top of you script Notice The Python wrapper requires Python 2 4 or above The following example is taken from MVD Scripting PythonWrapper SimpleDockingTest py import os import MvdWrapper create an output dir outputPath outputData complex lhvr if not os path exists outputPath os mkdir outputPath if os path exists outputPath and os path isdir outputPath print Created outputPath outputPath else raise IOError could not create path outputPath molegro virtual docker user manual 17 Script Interface page 197 251 Now start the wrapper Remember to change the path to the executable in the line below mvd MvdWrapper MvdWrapper C Program Files Molegro MVD bin mvdconsole exe gui True mvd info testing mvd random 123232 set the seed mvd cd outputPath change to output p
40. command enables a subset of the constraints in the workspace All constraints not specified in the list are not used during the docking run To disable all constraints set integer list NONE It is possible to specify ranges or to just enable all constraints by setting integer list ALL Notice the numbering of constraints is zero based meaning that the first constraint in a workspace will have number 0 the second number 1 and so forth Examples CONSTRAINTS 1 2 Enables the second and third constraint in the workspace All other constraints are disabled CONSTRAINTS 1 3 5 Enables the second fourth fifth and sixth constraint in the workspace All other constraints are disabled CONSTRAINTS NONE Disables all constraints in the workspace CONSTRAINTS ALL Enables all constraints in the workspace default behavior molegro virtual docker user manual 28 Appendix XI Script Commands page 240 251 RMSD lt targetligand gt The RMSD can be used to set a ligand to compare docking results with The Root Mean Square Deviation between heavy atoms will be calculated for all returned poses Notice the ligand used as reference for RMSD calculations must have the same number of heavy atoms as the ligands that are docked otherwise the RMSD calculation will just return 1 Examples LOAD 3PTB MVDML RMSD ligand 1 DO
41. conformation of the molecule 3D descriptors Molecular descriptors are typically fast to calculate for instance the topological CFDM descriptors described later can be calculated for more than 1000 compounds per minute This makes molecular descriptors very useful for e g initial filtering or clustering of a molecule library MVD is able to calculate molecular descriptors for all types of structural files that can be imported into the GUI or read from a Data Source e g PDB Mol2 MVDML SDF AS of now MVD does not parse SMILES strings or other 2D representations of molecules even though the molecular descriptors in MVD are dependent only on the 2D properties of the molecule The descriptor calculation wizard can be invoked from the main menu by choosing Tools Descriptors Calculation Wizard The first step is to specify which molecules the descriptors should be calculated for This selection interface is identical to the one in the Docking Wizard It is possible to calculate descriptors for molecules in the current workspace or from a chosen Data Source molegro virtual docker user manual 14 Molecular Descriptor Calculations page 171 251 Step 1 3 Choose Molecules From workspace L Cofactors 0 2 From extemal data source Uatasource Back Figure 110 Choosing molecules in the Descriptor Calculation Wizard When calculating molecular descriptors for a large set of
42. count Energy terms contributions E Total The total MolDock Score energy is the sum of internal ligand energies protein interaction energies and soft penalties E Inter total The total MolDock Score interaction energy between the pose and the target molecule s E Inter cofactor ligand The total MolDock Score interaction energy between the pose and the cofactors The sum of the steric interaction energies calculated by PLP and the electric and hydrogen bonding terms below Cofactor VdW The steric interaction energy between the pose and the cofactors calculated using a LJ12 6 approximation Notice This term is not used by the MolDock score Cofactor elec The electrostatic interaction energy between the pose and the cofactors Cofactor hbond The hydrogen bonding interaction energy between the pose and the cofactors calculated by PLP E Inter protein ligand The MolDock Score interaction energy between the pose and the protein Equal to SterictHBond Electro ElectroLong below Steric Steric interaction energy between the protein and the ligand calculated by PLP HBond Hydrogen bonding energy between protein and ligand calculated by PLP Electro The short range r lt 4 5A electrostatic protein ligand interaction energy ElectroLong The long range r gt 4 5A electrostatic protein ligand interaction energy NoHBond90 This is the hydrogen bon
43. data sources These can be used when the input structures are split over several different files A multifile data source may contain files with a mixture of different data formats molegro virtual docker user manual 5 Data Sources page 82 251 File data sources are identified by a File identifier Examples File fileserver molecules mol23 mol2 File C Test Molecules steroids sdf Index 2 4 8 12 34 It is possible to import a subset of the structures in a file using the Index specifier Molecules must be separated either by for SDF files or lt TRIPOS gt MOLECULE for multi molecule Mol2 files Only one molecule will be extracted from each section separated by these separators For PDB files only the first HETATM molecule will be imported Notices that all input structures are expected to be ligands Molecules recognized as proteins or water molecules will be ignored The optional Index specifier must be a comma separated list of either single values or intervals Notice that open intervals are allowed e g 5 or 19 Indices should be ordered strictly increasing Invalid or non existent indices will be ignored The Index specifier is 1 based the number of the first molecule is 1 and not 0 Filenames containing spaces must be enclosed in quotation marks It is possible to specify files on shared network drives and folders Multifile data sources are identified by a Dir identifie
44. default OpenGL rendering for instance spheres are not converted into triangle meshes before being drawn and it possible to create shadow effects Since another rendering technique is used the output may deviate from the OpenGL view The High Quality Render also makes it possible to create high resolution images suitable for publications Notice that a few graphical objects are not supported by the raytracer dot surfaces protonation guides and energy grids The raytracer also ignores clipping planes and the light source settings in the Visualization Settings Dialog molegro virtual docker user manual 3 User Interface page 57 251 Pixel size Width pixels Height pixels Double size Half size Window size Physical size Resolution DPI 300 00 Units inches Width inches 1 29 Z Create shadows Font scale 1 00 Adaptive antialias Low 4 samples per pixel coe Figure 45 The High Quality Output dialog The High Quality Output dialog controls the size and rendering options It is possible to specify an image size in either pixels or physical units In order to use physical units it is necessary to specify the printing resolution of the physical media the default resolution is 300 DPI dots per inch It is possible to choose between inches and cm as units but the DPI is always specified in inches Shadows can be toggled on and off and it is possible to specify a font s
45. docking with Molegro Virtual Docker will be successful or not By taking the following suggestions into account we hope that common pitfalls can be avoided a General issues It is recommended to remove unwanted material such as proteins ligands cofactors and water molecules if they are not needed in the actual docking simulation a Validation The automatic preparation of molecules might fail in some cases It is therefore advisable to manually inspect the molecules in particular ligands and check bond orders hybridization states and if hydrogens are correctly assigned a Protonation If the protein is expected to have unusual protonation states near the binding site be sure to set them using the Protein Preparation dialog a Ligand flexibility By default all torsions in the ligand that can be flexible are set flexible during the docking simulation The complexity of the docking search can be significantly reduced if the number of torsions that are set flexible during the docking run is lowered Bonds can be set rigid during docking using the context menu right click on the bond and select Set Flexibility Rigid while docking a Cavity detection Before starting the docking run all potential binding sites active sites should be identified using the Detect Cavities dialog The default settings listed in the wizard are generally applicable molegro virtual docker user manual 12 Obtaining the Best Docking Results page
46. down menu The different choices for multiple atoms are All meaning all atoms None which causes the constraints to try to remove atoms within the constraint range Hydrogen Donor Hydrogen Acceptor Hydrogen Donor or Acceptor Both Non polar and Ring Atoms atoms in aromatic or aliphatic rings Additionally it is also possible to specify ligand atoms from a current selection of atoms using the Specify atoms for each ligand option and pressing the Define from selected atoms button This also applies to more than one ligand which makes it easier to constrain specific atoms for a set of ligands present in the workspace The View list button can be used to inspect the current set of selected ligand atoms A Hard constraint see above range can be specified If this is enabled the docking engine will try to force the selected ligand atoms to be within this range The bottom panel Soft constraint allows the user to specify a specific potential applied to the selected ligand atoms The potential is a piece wise linear potential which is the same type as used in the docking score function see Appendix I MolDock Scoring Function It is shown graphically in the graph at the bottom When applying soft constraints the following procedure is used for all chosen ligand atoms as defined by the Ligands atoms of Type or Specific ligand atom input fields the distance between the center of the constraint and the atom is calculated The potent
47. each pose returned by the docking engine For each residue LocalSteps iterations of energy minimization using a Nelder Mead Simplex algorithm is performed for each residue After that GlobalSteps iterations are performed on all residues at once again using the Nelder Mead Simplex algorithm Receptor minimization is normally used together with a softening of the potentials and Tabu Clustering If Receptor minimization is enabled a copy of the minimized receptor configuration is saved together with the pose for each found solution The receptor configurations will be saved as ligandname receptorConfiguration and are most easily inspected using the Pose Organizer postMinimize Perform short energy minimization of final poses found after docking See Section 6 3 for details Default value is false postOptimizeHBonds Optimize hydrogen donor positions both for pose and protein target atoms See Section 6 3 for details Default value is true The default settings corresponds to the following script command DOCKSETTINGS maxIterations 2000 runs 1 ignoreSimilarPoses true IgnoreSimilarPosesThreshold 1 0 MaxPoses 5 postMinimize false poseOptimizeHBonds true It is not necessary to specify all of the parameters If only some of them are molegro virtual docker user manual 28 Appendix XI Script Commands page 238 251 DOCKSETTTINGS lt initstring gt specified the default parameters will be
48. force fields in Molegro Virtual Docker using the Energy Map Visualization dialog The Energy Map Visualization dialog can be invoked by pressing the Energy Map button on the main GUI toolbar molegro virtual docker user manual 3 User Interface page 65 251 1HVR mvdml Molegro Virtual Docker File Edt View Rendering Preparation Docking Tools Window Help amp B C Q BB Hetogens Fog Hide Residues Search Space _ Ligand Map_ Eneray Map fear Options S Workspace New amp Backbones 2 a Cavities 1 a C Cofactors 2 E Constraints 1 a Z Energy Map 1 a Ligands 51 S C Proteins 2 a O Surfaces 2 Energy Grid MolDock Score GRID V Steric Favorable J Hydrogen Acceptor Favorable Property Value i 7 Hydrogen Donor Favorable Selected Atoms 36 WF Glechostatic Threshold Dot Size Clear Selection Time Description 14 15 34 268 Process spawned 14 35 17 326 Energy Maps work better when there is no transparent objects Tumed off Search Space 14 35 17 334 Found grid in workspace 14 35 17 335 Started creating grid Radius 15 Resolution 0 55 Points per side 55 Total points 166375 Layers 5 Mem 6 35 14 35 18 231 Created grid with 166375 points 1514 atoms 12515261 entries written 14 36 04 977 Building secondary structure 3d object with 8 regions 14 36 05 017 Building secondary structure 3d object
49. gt Dock File ZINC00006989 mvdml lt Unit gt lt After gt DONE lt After gt lt Job gt The Job id tag is a simple identifier It can be any text string but it must be unique The description tag can be used for arbitrary remarks it is not used by the Virtual Grid infrastructure The grid job description consists of a lt Before gt element any number of lt Unit gt elements and an lt After gt element The content of these tags are script commands for the MVD script parser An agent will execute one unit per processing thread per default an agent simultaneously execute one unit per physical CPU core Whenever an unit is executed on an agent the script content in the lt Before gt element is executed followed by the content in the particular lt Unit gt element being executed finally followed by the content in the lt After gt element The lt Before gt and lt Unit gt elements also specify an uploadFiles attribute which list the files that must be uploaded to the agent before starting the job The agent will automatically keep track of which files are produced by MVD and return them to the controller The easiest way to create a custom grid job file is to setup a MVG job using the Docking Wizard and manually edit the saved script The grid job file must be saved in a file with a gridjob extension All input files must be located in
50. in the residue their hybridization element type partial charge and their number of hydrogens The base protonation also describes the bonds in the residue and the order of these bonds The base protonation is described by the lt Atom gt and lt Bond gt elements that are immediate children of the lt Residue gt element A residue may also contain a number of a ternative protonations These are described by the lt Protonation gt elements The alternate protonation are considered modifications to the base protonation so they describe only the differences to the base protonation Any lt Atom gt or lt Bond gt tag in an alternate protonation description will replace the settings inherited from the base protonation A short description of the various attributes is shown in the table below molegro virtual docker user manual 4 Preparation page 80 251 lt Residue gt The name attribute is used to identify the residues in a PDB file The other attributes letter longName and pdbAlias are purely informational and not used during parsing lt Atom gt pdbName is used to identify the atom in the PDB file hyb describes the hybridization of the atom 2 SP2 and 3 SP3 Charge is the atomic partial charge Hydrogen is the number of hydrogens attached to this atom Element is the element type lt Bond gt from and to must be pdbNames of the atoms thi
51. lt 4 5A ElectroLong Long range electrostatic protein ligand interations r gt 4 54 HBond Hydrogen bonding energy Heavy Atoms Number of heavy atoms in ligand MW Molecular weight in dalton LE1 Ligand Efficiency 1 MolDock Score divided by Heavy Atoms count LE3 Ligand Efficiency 3 Rerank Score divided by Heavy Atoms count molegro virtual docker user manual page 116 251 7 Analyzing the Docking Results page 117 251 Column Name Description Docking Score Evaluated before post processing either Plants or MolDock This is the PoseEnergy term in a mvdresults file Similarity Score The similarity score if docking with templates DisplacedWater The energy contributions from non displaced and displaced water interactions if enabled SMILES Contains connectivity information useful for 2D depictions Table 1 Column names available in the Pose Organizer dialog After importing and preparing molecules all information can be saved in a MVD Workspace MVDML file which contains all relevant information position of atoms charges hybridization bond orders ligand flexibility To save a workspace select File Save Workspace As Alternatively use the keyboard shortcut Ctrl S Notice Visualization objects surfaces labels interactions are not saved in MVDML files The Export Molecules dialog can be used to export al
52. molecules it is always advisable to use the data source import since importing large molecule libraries into the graphical user interface requires all molecules to be present in memory at once and will slow the system Most of the molecular descriptors in MVD can only be calculated for small molecules and will automatically skip the calculation for proteins Also notice that when importing molecules from an external data source in PDB format only the ligands in the file are imported protein cofactors and water molecules are ignores 14 2 Descriptors in MVD The next step is to choose which descriptors to calculate molegro virtual docker user manual 14 Molecular Descriptor Calculations page 172 251 s Descriptor Calculation Step 2 3 Choose Which Descriptors to Calculate 76 chosen Descriptors Ligand Name SMILES Element Count Simple Descriptors 9 Andrews Affinity Tems 12 Chemical Feature Distance Matrix 45 Wiener Index 1 SMILES Creates a SMILES representation of a ligand This makes it possible to visualize the molecule in the Data Analyzer and in Molegro Data Modeller MDM Configure Ge e Figure 111 Choosing descriptors in the Descriptor Calculation Wizard The following categories of descriptors are available Category Details Ligand Name Not a numerical descriptor simply adds a column with the name of the compound to the output SMILES Creates a SM
53. new updates on startup option enables MVD to automatically check for new updates during startup a The Create system log in directory below option is used to toggle whether a system log is created for each execution of MVD The system log contains information about user actions conducted and is used to track potential bugs and performance problems By default the log files are stored in the Logs directory located in the same directory as the mvd executable file but another directory can be used if needed e g if user has no write permissions to the directory used Notice If you encounter problems with MVD please email the log file created before the crash to support clcbio com a The Working directory setting is used to set the current Working directory which is the root path for file related operators e g when loading and saving molecular structure files and log files a The Virtual Grid executable and PDF viewer settings are used to molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 158 251 specify the location of the executable files for Molegro Virtual Grid and a PDF viewer for reading the user manual The default PDF viewer specified by the operating system will be used if no executable file is provided a The CUDA device setting is used to specify default CUDA device ID See Section 6 5 for more details a The Level of details for docking file logs option is used to specify the level a
54. on the Visualization Settings dialog allows you to customize the rendering behavior molegro virtual docker user manual 3 User Interface page 53 251 Visualization Setting Views Fog Lights 7 Enable fog linear Near f i 3D Projection Perspective Angle Light 1 Ambient _ Diffuse Global Coloring Specular Background Color Label Color Cavity Color Restore to Default Settings Figure 42 The Visualization Settings Rendering options The Fog settings enables or disables fog It is possible to adjust when the fog should begin the Near value and when the fog should reach its maximum density the Far value The 3D Projection settings manage the perspective projection In Perspective projection objects farther away from the viewer appear smaller the magnitude of this effect can be controlled by adjusting the field of view Angle parameter In Orthographic projection object sizes are independent of their distance from the viewer The Global Coloring settings allow you to adjust the background color the color labels are drawn with and the color cavities predicted binding pockets are drawn with The Lights section controls the global lightning of the 3D world It is possible to enable one or two light sources Their positions can be adjusted directly in the 3D sphere view The light source color can be changed by clicking the color molegro virtual docker user manua
55. on the docking icon gear wheel on the tool bar Additionally the keyboard shortcut F1 is available Notice In order to initiate the docking at least one protein and one ligand molecule have to be present in the workspace Choose Which Ligands to Dock The first action is to choose which ligands to dock Choose Which Ligands to Dock From workspace W Ligands i BEN_1 A Proteins Cofactors WI CA_480 A Structural Water fi All waters From extemal data source Datasource From KNIME workflow Reference ligand for RMSD calculations None Figure 64 Select which ligands to dock If more than one ligand is available in the workspace the user can select which ones to use by clicking on the corresponding molecules in the window If more than one ligand is selected all selected ligands will be docked one ata time Water molecules and cofactors if any are always included in the docking molegro virtual docker user manual 6 Docking Functionality page 92 251 simulation remember to remove them from the workspace if they should not be included Moreover a reference ligand can be specified at the bottom The reference ligand is used to calculate the root mean squared deviation RMSD between the reference ligand and the docked pose The reference ligand or ligands are only available if they are compatible w r t symmetry identical number of heavy atoms etc wit
56. open the Visualization Settings Dialoq make the desired changes and select Use as Default Settings Reset All to Defaults Figure 105 The graphics tab of the Preferences dialog a The Show pivot point rotational center option toggles the visibility of the pivot point small grayish ball a The Show root atom option toggles the visibility of the currently chosen root atom for each of the ligands in the workspace see Set root atom in Section 4 3 for more info The Fade 3D labels when in background option toggles fading of labels in the Visualization Window a The overall rendering quality can be specified using the Quality option Modern computers with dedicated 3D hardware should be able to run at highest quality even when rendering relatively large molecules It is easy to test new quality settings by selecting the level of quality and pressing the Apply button molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 160 251 Parsing Mouse wheel model Generic Mouse F Invert zoom direction Wheel rotation speed 1 Wheel zoom speed 0 5 Reset All to Defaults Figure 106 Mouse Preferences The Mouse tab customizes how the mouse interacts with the 3D world MVD supports the 360 degrees scroll ball on the Apple Mighty Mouse Currently the 360 degrees scroll bar feature is only supported on Mac OS X since no mouse drivers are available for
57. or using Docking Pose Organizer if poses are present in the Workspace Explorer When the Pose Organizer is invoked it displays a list of poses parsed from the mvdresults file or poses currently in the workspace The table in the middle of the dialog window shows various columns with information about different energy contributions and other data for each pose The columns can be changed under the Settings tab pane A panel in the bottom of the dialog Sorting Criteria allows the user to sort the table by up to three different criteria By default the table in the middle supports multiple selection i e more than one pose can be highlighted Only highlighted poses will be visible in the 3D window This setting is useful for quick comparison of different poses molegro virtual docker user manual 7 Analyzing the Docking Results page 111 251 This default behavior can be changed by selecting Dynamic update notice disables multiple poses selection In this mode only one pose is shown at a time In return it offers the possibility to visualize different interactions for the current selected pose e g hydrogen bonds Even though Dynamic Update is a single selection mode it is possible to lock poses which keeps them visible even when not selected A pose can be locked by using the context menu on its entry in the table and selecting Lock or Unlock Locking is purely a visualization aid and has no other consequences for the pose
58. other platforms but the mouse still works as a generic mouse on Windows and Linux To enable Apple Mighty Mouse support select it under Mouse wheel model When Apple Mighty Mouse mode is selected the scroll ball can be used to rotate the 3D world Additionally the scroll ball button can be used to zoom in the 3D world by pressing the button while using the scroll ball as a standard mouse wheel However to enable the zoom option the scroll ball button should be set to Button 3 in the Mac OS X Mouse preferences dialog see Figure 107 Invert zoom direction toggles how the 3D worlds zooms rotating the scroll wheel towards the user will normally make the 3D objects appear larger but this behavior can be inverted by toggling this option on The setting also applies to zooming using both mouse buttons molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 161 251 It is also possible to adjust the mouse wheel sensitivity by using the Wheel rotation speed and Wheel zoom speed sliders Keyboard amp Mouse a gt Showall Q Keyboard Trackpad Mouse Bluetooth Keyboard Shortcuts Button 3 2 Primary Button 24 Secondary Button B Expos All Windows B Scrolling Options 360 Degree B Tracking Scrolling Double Click EA NEA I AE 1 I I a tp i Yi Slow Fast Slow Fast Slow Fast V Zoom using scroll ball while holding Control jej Options Figure 107 Migh
59. search algorithm choose Search algorithm gt Algorithm gt Iterated Simplex from the Docking Wizard The following parameters can be set Max iterations default 100 The number of steps per run Population size default 20 The number of individuals sampled during each iteration of the algorithm Maximum Steps default 2000 The number of iterations of the Nelder Mead simplex minimization procedure performed for each individual in the population Tolerance default 0 01 Tolerance iteration best solution default 0 0001 The Iterated Simplex algorithm can use an adaptive sampling strategy based on Ant Colony Optimization ACO The idea in ACO is to use pheromone trails to bias the initialization of individuals towards regions previously resulting in good solutions The pheromone trails are updated in each iteration of the search algorithm based on the currently best found solution The parameters Evaporation rate and Probability of best ant pBest are used to control how much the pheromones are modified For more details about ACO and the parameters see KORB 2009 By default adaptive sampling is not enabled in MVD since it did not produce better docking results when including pheromone trails benchmarked on 85 complexes Evaporation rate default 0 15 Probability of best ant pBest default 0 5 To use the Iterated Simplex search algorithm the OPTIMIZERTYPE script command has to be set Moreover spe
60. some cases the pre calculated Ewater other waters contributions might differ a bit compared with the actual contributions from the neighbouring water molecules since displaced water molecules are included The energy required to remove a water molecule iS Eremove water Ewater protein cofactor Ewater other waters Eentropy reward When a water molecule is displaced it gains rotational and translational degrees of freedom compared with its bound state when binding to a protein or a ligand Thus the Eentropy reward IS a reward representing the gain in entropy that occurs when a water molecule is displaced since a system will always favor states with higher entropy according to Gibbs free energy It can be difficult to determine the optimal entropy reward but it should be less than the contributions from a water molecule interacting with other molegro virtual docker user manual 9 Displaceable Water page 141 251 protein cofactor water atoms i e E entropy reward lt Ewater protein cofactor Ewater other waters The higher the entropy reward is the easier it gets to displace water molecules By default Eentropy rewara O but the entropy reward can be customized by the user Notice that the units for the entropy reward are arbitrary the entropy reward is not based on physical units The next step is to look at each water molecule during an evaluation of a ligand pose and decide if the water molecule should be displ
61. steps independently for each residue Maximum steps per residue and afterwards performing a global minimization run on all residues simultaneously Maximum global steps The minimization procedure is started by pressing the Minimize button After the minimization procedure completes a new receptor conformation will be added to the workspace usually it takes just a few seconds but this depends on the number of residues being minimized Also notice that new columns are added to the sidechain list after the minimization has completed E_before which is the energy before the sidechain has been minimized E_after which is the energy after and dE which is the difference in energy Notice that these energies are not measured in chemically relevant units and that their magnitude will depend on which structures were taken into account during the minimization When docking with sidechain flexibility or after sidechain minimizations have been conducted new receptor conformations are added to the workspace A receptor conformation is a list of torsional changes to an existing receptor which can be one or more proteins chains each protein chain will have its own entry under Proteins in the Workspace Explorer Notice that a receptor conformation is not an isolated entity it always exists in the context of one or more proteins or protein chains When new receptor conformations are added to the workspace they will appear in a drop down box in
62. the grid manually see Section 15 8 for more information After the machines in the grid have been detected or manually specified the actual communication between the controller and agent takes place via TCP traffic on port 45454 Notice that many modern operating systems provide some kind of firewall which prevents software from receiving requests on arbitrary ports The Virtual Grid Agent acts like a web server which listens for requests on port 45454 This means if a firewall is present it must allow incoming connections for this port The actual details on how to configure firewall access depends on the specific operating system For instance on Windows Vista the firewall can be configured using Start Menu Control Panel Security Allow a program though Windows Firewall and choosing Add port The following settings molegro virtual docker user manual 15 Molegro Virtual Grid page 181 251 can then be used Name Virtual Grid Port number 45454 and protocol TCP The physical network the machine belongs to may also have a firewall which prevents communication with other networks If you need to communicate with a Molegro Virtual Grid on another network we strongly suggest that you use VPN to setup the connection Please see the previous section for more details All licenses for Molegro Virtual Docker include a basic license for Molegro Virtual Grid The basic license makes it possible to run jobs on only one 1 agent
63. the protein We will do this by choosing Create Surface from the Proteins context menu in the Workspace Explorer see Figure 7 molegro virtual docker user manual 2 Docking Tutorial page 16 251 items Options v Workspace New Cavities 1 Cofactors 2 O Constraints 1 Ligands 1 Pr Proteins v Create Suface O Create Backbone Visualization Create Labels Te a Invert Selection Remove Checked Proteins From Workspace Property Remove All Proteins From Workspace Detect Cavities Prepare All Proteins n Figure 7 Surface creation In the dialog that appears just click OK This will create a protein surface based on the default settings which are an opaque solvent accessible surface colored according to the electrostatic potential red and blue colored areas correspond to regions with respectively negatively and positively charged residues Notice that the surface also show up as an element in the Workspace Explorer Surfaces category Next we will try to narrow down the potential binding site for the protein This can be done automatically by selecting Preparation Detect Cavities After pressing the OK button the system will predict a binding site in the center of the protein see Figure 8 using the algorithm described in Appendix IV Cavity Prediction molegro virtual docker user manual 2 Docking Tutorial page 17 251 x gt Figure 8 The predicte
64. the sphere Bond Scale is the diameter of the bonds in Angstrom This is the preferred graphical style for modifying and inspecting bond and atom properties since the bond order is visualized and the atoms are easy to select Stick Bonds are drawn as cylinders Bond Scale is the diameter of the bonds in Angstrom Spacefill CPK Atoms are drawn as spheres balls Bonds are not drawn The Atom Scale parameter sets the fraction of the Van der Waals radius that is used as radius for the sphere Wireframe This is by far the fastest way to draw molecules Bonds are drawn as lines between atoms No atoms are drawn but notice that it is still possible to do atom selections in the GUI Notice all bonds are drawn as single lines double bonds and delocalized bonds are also drawn as single lines It is possible to adjust the line width in pixels Notice that not all OpenGL implementations support non integer line widths The following coloring styles can be applied to all molecules Fixed Color A user defined color Color By Element CPK Atoms are colored according to element type Color By Id or Chain Molecules are colored according to their internal molecule ID i e a single ligand will be uniformly colored but all ligands will have different colors Color By Id carbons only Same as above except only carbons are colored using this scheme Other atoms are colored according to element type Color By Hydrogen Bond Ty
65. to Defaults Figure 108 Parsing preferences The Default File Encoding drop down box allows you to choose which encoding should be used It is recommended to use the default setting UTF 8 Unicode Using the UTF 8 encoding all Unicode characters can be encoded and since molecular data files rarely contain special characters it is more space efficient than UTF 16 where each character always uses at least 2 bytes Files stored as 8 bit ANSI ASCII files will also be imported correctly as Unicode if they do not contain any special national characters and UTF 16 will also be automatically recognized in this mode It is also possible to store data as Locale 8 bit In this encoding all characters are stored as a single byte meaning only 256 characters can be represented The actual characters included in this set depends on the current national codepage settings on the machine This option should only be used when exporting data to older software products not capable of parsing Unicode text Break unrealistic bonds during import Mol2 SDF determines whether or not unrealistic bonds parsed from Mol2 or SDF files should be ignored during import A bond is considered unrealistic if the distance between two bonded atoms is more than the sum of their covalent radii plus a threshold of 0 74 molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 163 251 The Combine Mol2 substructures and small PDB molecules with same
66. to copy the table to the clipboard for further inspection in an external text editor or spreadsheet molegro virtual docker user manual 8 Sidechain Flexibility It is possible to work with sidechain conformational changes in two ways a By softening the potentials the steric hydrogen bonding and electrostatic forces used during the docking simulation This is done in order to simulate flexibility in the binding pocket induced fit a By defining which residues should be considered flexible during the docking simulation The backbone is kept rigid but the torsional angles in the sidechains are allowed to change When sidechain flexibility has been setup the following steps are applied during the docking simulation a The ligands will be docked with the softened potentials At this point the receptor is kept rigid at its default conformation a After each ligand has been docked the sidechains chosen for minimization will be minimized with respect to the found pose After repositioning the sidechains the ligand will be energy minimized The repositioning of the sidechains and minimization of the ligand will be performed using the standard non softened potentials It is preferable to use the Tabu Clustering algorithm in order to ensure a greater diversity of the found poses during the docking simulation see Section 6 3 Also notice that only the MolDock GRID potential supports softened potentials The Mo
67. water molecules is done during the evaluation of the protein ligand binding and is thus separated from the conformational sampling While the displaceable water model may be successful in some cases where ordinary docking fails it also has some restrictions see below Therefore we recommend to use the displaceable water model in situations where docking without water is not successful In addition the model requires a priori knowledge of likely water molecule positions something which is not always available Restrictions a MVD cannot predict water positions in the binding site If possible the water molecules should be obtained from an apo structure since a holo structure containing a co crystallized ligand might already have displaced the water molecules Another possibility is to use other third party software products to predict or identify relevant positions of water molecules m Search space Even though no additional degrees of freedom are molegro virtual docker user manual 9 Displaceable Water page 140 251 introduced when using the displaceable water model in MVD the search space may be less predictable resulting in poorer performance If needed increasing the number of docking runs can improve the performance m Speed Enabling the displaceable water model increases the docking runtime dependent on the number of water molecules in the workspace Therefore we recommend to focus on a selected subset of water mo
68. 0O3 0 33 O atoms in S03 1 0 N atoms in SO2NH Table 3 Charge templates Epp is a piecewise linear potential using two different sets of parameters One set for approximating the steric Van der Waals term between atoms and another stronger potential for hydrogen bonds The linear potential is defined by the following functional form Ep p O Ao Epip R1 0 Epip R2 Ep p R3 Ep p r Oforr R and is linearly interpolated between these values The parameters used here see Table 4 were adopted from GEMDOCK YANG 2004 Ao A1 Ri R2 R3 R4 hydrogen bond 20 0 2 5 2 3 2 6 3 1 3 6 steric 20 0 0 4 3 3 3 6 4 5 6 0 Table 4 PLP parameters A bond is considered a hydrogen bond if one of the atoms can donate a hydrogen atom and the other atom can accept it The atom types are assigned according to the scheme shown in Table 5 molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 200 251 type atoms acceptor N and O with no Hs attached donor N and S with one or more Hs attached both O with one H attached or O in water molecules nonpolar all other atoms Table 5 Hydrogen bond types The PLP hydrogen bond term mentioned above only depends on the distance between atoms In order to take into account the directionality of the hydrogen bonding the geometry of the hydrogen bond is examined and the following factor Hractor is Multiplied to the PLP hy
69. 1 The columns in the list can be toggled on and off using the context menu on the list view The Tolerance of a potential refers to the size of the region between a ligand atom and a receptor atom where the interaction energy is optimal For non polar steric interactions such as two carbon atoms the interaction is optimal between 3 6 A and 4 5 A see Appendix I MolDock Scoring Function for more information about the scoring function This gives a tolerance of 0 9 A If the tolerance is increased to e g 1 5 A the interaction would be optimal at distances between 3 3 A and 4 8 A Notice that the tolerance is only softened for atoms in the sidechain not for the backbone atoms Also changing the tolerance only affects pairwise steric and hydrogen bonding potentials electrostatic forces are not changed The Strength factor is multiplied onto all interaction energies for the sidechain atomic pairwise steric interactions hydrogen bondings and electrostatic interactions If a sidechain is known to be very flexible set its strength to zero in order to turn all its interactions off during the docking simulation Notice that the strength factor does not change the interactions of the backbone atom After choosing a number of sidechains and configuring their flexibility options press OK to add a sidechain flexibility description to the workspace A new category will appear in the Workspace Explorer Flexible Residues and the selected sidechai
70. 120 providing useful tips on how to use Molegro Virtual Docker is available Q Did you know Ligand flexibility By default all torsions in the ligand that can be flexible are set flexible during the docking simulation The complexity of the docking search can be significantly reduced if the number of torsions that are set flexible during the docking run is lowered Bonds can be set rigid during docking using the context menu right click on the bond and select Set Flexibility Rigid while docking E Show tips at startup Next Tip Figure 120 Tip of the Day dialog molegro virtual docker user manual 16 Help page 192 251 The dialog can be manually invoked from the Help menu or automatically shown on startup The automatic startup setting can be toggled in the dialog or from the general Preferences dialog The Molegro website also offers certain help facilities Please visit www molegro com to see our FAQs and other information available Technical support is available for commercial licenses industrial and academic only To obtain additional support send an email to support clcbio com molegro virtual docker user manual 1 Script Interface The default behavior for docking molecules in Molegro Virtual Docker is to start the application load and prepare the molecules and invoke the Docking Wizard The Docking Wizard guides the user through the different settings for the simulat
71. By atom ID fast Virtual screening mode Keep atleasttop 10 00 percent o contain the top n percent bes Notice The retumed set i ranteed t g but filteri one during the screening so more than the chosen ill be retume Figure 69 Pose clustering options Notice The actual number of poses returned may be lower than the maximum number of poses specified in Max number of poses returned For instance the energy or clustering threshold options can reduce the number of poses returned if poses have higher energies or are too similar However the overall best scoring pose will always be returned If only one pose is returned per run Return one pose for each run a special clustering technique called Tabu Clustering can be applied When using this clustering technique each found solution is added to a tabu list during the docking simulation the poses are compared to the ligands in this tabu list If the pose being docked is closer to one of the ligands in the molegro virtual docker user manual 6 Docking Functionality page 99 251 list than specified by the RMSD treshold an extra penalty term the Energy penalty is added to the scoring function This ensures a greater diversity of the returned solutions since the docking engine will focus its search on poses different from earlier poses found It is possible to specify whether RMSD calculations should be performed by comparing atom ID which is the fastest c
72. CK Docks the ligands in 3PTB MVDML and calculate their RMSD deviation from ligand 1 which is the second ligand present in the workspace TEMPLATE parameters The TEMPLATE command is used to specify parameters for template docking The following parameters are available strength the normalization constant for a perfect match to the template Default value is 500 useGrid determines if template force field should be precalculated ona grid Default is true gridResolution the resolution of the template force field grid Default is 0 4 measured in A Example TEMPLATE strength 500 useGrid true gridResolution 0 4 ADDWATER lt x y z gt The ADDWATER command is used to create a water molecule at the position specified and add it to the current workspace Example AddWater 2 4 1 5 7 8 molegro virtual docker user manual 28 Appendix XI Script Commands page 241 251 DOWNLOAD lt PDB code gt AS lt filename pdb gt The DOWNLOAD command can be used to download a PDB file from the Protein Data Bank The downloaded file will be saved as lt filename pdb gt The downloaded PDB file is not automatically imported to the current workspace This should be done using the IMPORT command Notice the lt PDB code gt is a 4 letter PDB identifier and that the filename should include the pdb file extension Moreover the DOWNLOAD command overwr
73. Color by structure colors the backbone based on the secondary structure information alpha helices are colored yellow beta sheets are colored blue and coil is colored gray Color by residue position colors the backbone based on the residues order of occurrence creating a rainbow color effect Color by chain colors each individual protein chain in a different color Color by atom colors the backbone by using the currently shown color of the protein backbone atoms the color used is taken from the C alpha atom On the advanced panel the Color interpolation check box allows you to determine whether the backbone color should be interpolated between the atoms it passes through or should be held constant between atoms Diameter A sets the width of the backbone in angstrom Subdivision sets the resolution of the backbone the number of subdivisions between each residue in the protein Backbones appear in the Backbones category in the Workspace Explorer and can be removed via the context menu or hidden using the check box molegro virtual docker user manual 3 User Interface page 45 251 3 19 Making Screenshots Screenshots can be made by choosing Window Capture Screen Figure 36 Screen Capture dialog It is possible to specify whether to capture the Visualization Window only the 3D view or the entire Desktop see Figure 36 The captured region can be saved in JPG BMP or PNG file formats 3 20 Sidechain Minimization
74. ILES string suitable for 2D representations SMILES strings can be visualized as 2D molecule depictions in Molegro Data Modeller Element Count Counts the number of atoms for a given element By default H C N O P and S are counted All other elements are counted as other The elements may be customized using the Configure button Simple Descriptors A set of common descriptors including molecular weight hydrogen donor acceptor count and other simple descriptors The available descriptors are molegro virtual docker user manual 14 Molecular Descriptor Calculations page 173 251 MW Molecular Weight Atoms Atom count including hydrogens HeavyAtoms Atom count excluding hydrogens Rot The number of rotatable bonds Rot2 The number of rotatable bonds but excluding any bonds which only rotates terminal hydrogen atoms HD The number of hydrogen donors HA The number of hydrogen acceptors Rings The number of rings Aro The number of aromatic rings Andrews Affinity Terms An Andrews Affinity measure together with the terms needed for the calculation These terms are described in Functional goup contributions to drug receptor interactions PR Andrews DJ Craik JL Martin Journal of medicinal chemistry 27 1212 1648 1657 American Chemical Society 1984 Chemical Feature Distance Matrix The CFDM descriptors were created by Molegro and are described in detai
75. MVD Data DockingOutput 226 Current ligand 2 10 runs ae Log Poses current ligand 1 Poses all Graph Current script Time 10 12 02 075 10 12 02 100 10 12 02 112 10 12 02 113 10 12 02 115 10 12 02 124 10 12 02 126 10 12 02 155 10 12 02 157 10 12 02 180 10 12 02 181 10 12 02 285 10 12 02 305 10 12 02 477 10 12 02 571 10 12 02 794 Pose 0 Name BEN_1 A Energy 100 026 RMSD 0 Added ligand BEN_1 A 1 100 026 Beginning run 2 out of 10 Source Ligand was randomized This will destroy its original orientation Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStudio Release Misc Data s Reading 626 values Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStudio Release Misc Data s Reading 2378 values Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStudio Release Misc Data s Reading 1868 values We are docking from the current active ligand BEN_1 A Number of cavity positions retumed 94 Tuming off construction of new poses iteration 1 Iteration 10 Lowest Energy 100 006 Iteration 30 Lowest Energy 100 036 Iteration 90 Lowest Energy 100 043 Status Docking BEN_1 AJ from Unnamed_complex mvdmi Figure 72 Docking Progress dialog The Graph tab shows the convergence of the population of candidate solutions The blue graph shows the energy of the best pose and
76. MVD allows you to minimize a protein with respect to itself and other structures in the workspace The minimization is performed using a fairly simple forcefield it uses the PLP potentials for steric and hydrogen bonding interactions and the Coulomb potential for the electrostatic forces as defined in Appendix I MolDock Scoring Function Only torsion angles in the sidechains are modified during the minimization all other properties including bond lengths and backbone atom positions are held fixed molegro virtual docker user manual 3 User Interface page 46 251 Sidechain Minimization Setup Advanced Sidechains to minimize Residue Protein ID Leu 300 0 2ACR A 4 Cys 298 0 2ACR A 2 3 4 Val 297 0 2ACR AJ Arg 296 0 2ACR A Lys262 0 2ACR A 5 Tp 219 0 2ACR AD 2 Arg 217 0 2ACRIA 4 17 41 Ser210 0 2ACR AD 2 5 92 Tur 209 0 MAR IAN 3 amp 55 Add Closest to Active Ligand Add Visible Add Selected aa Clear List Remove Selected Remove Non selected lt a Figure 37 The Sidechain Minimization dialog The Sidechain Minimization dialog can be invoked from Tools Sidechain Minimization see Figure 37 The Setup tab on the dialog controls which sidechains to minimize Several options exist for choosing the sidechains Add Closest to Active Ligand This will choose all sidechains which are close enough to the active ligand to interact with it
77. Notice MVD scripts need to have the mvdscript file extension Otherwise the script file will not be recognized and parsed by MVD It is also possible to start a script job with no graphical user interface without the script parsing progress dialog This can done by using the nogui command line argument Example mvd docktest mvdscript nogui Notice If you intend to run background jobs on remote Linux X11 systems use the nogui argument Otherwise the system might kill the process when the user logs off because the X11 server might be shutdown 17 3 Examples of Common Script Jobs This section contains some examples of common script jobs Another useful way of exploring the MVD script syntax is to inspect the script files generated molegro virtual docker user manual 17 Script Interface page 195 251 by the Docking Wizard these files are stored as ordinary MVD script files in the specified directory and can be opened using a standard text editor A complete list of commands can be found in Appendix XI Script Commands fy Tnit DOCKSETTINGS maxIterations 1000 runs 1 MaxPoses 5 EVALUATOR cropdistance 0 hbond90 true OPTIMIZER cavity true popsize 50 crossoverrate 0 9 keepmaxposes 5 Dock LOAD 3PTB MVDML RMSD ligand 0 DOCK Init DOCKSETTINGS maxIterations 1000 runs 1 MaxPoses 5 EVALUATOR cropdistance 0 hbond90 true OPTIMIZER cavity true popsize 50 crossoverrat
78. T Jackson P Jandu K S Rose V S Stables J N Structure Activity Relationships of Antifilarial Antimycin Analogues A Multivariate Pattern Recognition Study J Med Chem 1990 33 1 136 142 KORB 2009 Korb O Stutzle T Exner T E Empirical Scoring Functions for Advanced Protein Ligand Docking with PLANTS J Chem Inf Model 2009 49 1 84 96 CLARK 1989 Clark M Cramer III R D Opdenbosch N Van Validation of the General Purpose Tripos 5 2 Force Field J Comp Chem 1989 10 8 982 1012 molegro virtual docker user manual
79. The default settings corresponds to the following script command PARSERSETTINGS breakUnrealisticBonds false combineMoleculeFragments true useSybylForHybridiz ation true molegro virtual docker user manual 28 Appendix XI Script Commands page 237 251 DOCKSETTTINGS lt initstring gt Determines the behavior of the docking engine The settings string is composed of semi colon separated pairs of a parameter key and its corresponding value The different parameters are maxIterations the value must be an integer describing the maximum number of iterations by the MolDock engine The default value is 2000 runs the number of runs performed for each ligand Multiple runs will giver higher docking accuracy The default number is 1 Typically 5 to 10 runs are recommended ignoreSimilarPoses when running multiple runs several poses are returned for each ligand Set this to true to weed out similar poses by clustering according to their RMS deviation Default value is true IgnoreSimilarPosesThreshold This is the RMSD treshold value in Angstrom for the clustering described above Default value is true MaxPoses Determines the maximum number of poses returned by the clustering described above Default value is 5 MinimizeReceptor LocalSteps GlobalSteps Default is LocalSteps 0 GlobalSteps 0 corresponding to no minimization Enables minimization of the proteins in the workspace after
80. When inspecting poses obtained from different ligands the Only show top option can be used to focus on the most promising poses for each ligand The selection of the top poses are based on the currently chosen Sorting criteria Pressing the Open checked poses in Molegro Data Modeller button makes it possible to further inspect poses using the Molegro Data Modeller introduced in Chapter 13 Notice A detailed energy analysis is available by right clicking poses in the table and selecting Open Ligand Energy Inspector see Chapter 7 3 Additional options are available in the context menu allowing the user to select remove and export poses These options are also available from the File and Edit menus located in the Pose Organizer dialog molegro virtual docker user manual 7 Analyzing the Docking Results page 112 251 Pose Organizer 5 poses 00 BTN BTN_300 BTN_300 76 4451 71 9218 70 8064 GPU Score MolDock Score Rerank Score RMSD Only showtop 1 l poses for each ligand Open checked poses in Molegro Data Modeller Sorting criteria Pressing OK will keep 2 and ignore 3 poses Figure 76 The Pose Organizer dialog Dynamic update notice disables multiple poses selection 1st Ligand 2nd GPU Score The Settings Tab Pane of the Pose Organizer can be used to customize the Pose Organizer see Figure 77 molegro virtua
81. Y THE FOLLOWING TO CHAINS A REMARK 350 BIOMT1 1 1 000000 0 000000 0 000000 0 00000 REMARK 350 BIOMT2 1 0 000000 1 000000 0 000000 0 00000 REMARK 350 BIOMT3 1 0 000000 0 000000 1 000000 0 00000 4 b Notice Remove unwanted BIOMT transformations such as identity transformations before pressing OK Figure 47 The Biomolecule Generator The left panel on the dialog controls which molecules the transformation should be applied to This is normally the proteins or protein chains but ligands water and cofactors can also be transformed The right panel contains a text box where a transformation description can be pasted Notice that if a transformation remark was present in the last loaded PDB file it will automatically appear here It can be necessary to manually edit the transformation remarks For instance the remarks may contain redundant identity transformations which should be removed Example of identity transformation REMARK 350 BIOMT1 1 1 000000 0 000000 0 000000 0 00000 REMARK 350 BIOMT2 1 0 000000 1 000000 0 000000 0 00000 REMARK 350 BIOMT3 1 0 000000 0 000000 1 000000 0 00000 PDB transformation remarks are triplets of remark lines named BIOMT1 3 The first three columns constitute a rotation matrix and the last column is a translation vector For some complex structures the transformation description may contain several steps where different transformations are applied to d
82. a v Backbone style Cartoon Color scheme Color by structure Figure 33 Creating a new backbone The Create Backbone Visualization dialog allows you to select which proteins or protein chains the backbone should be visualized for Three main graphics styles can be used The Cartoon style visualizes the molegro virtual docker user manual 3 User Interface page 43 251 secondary structure of the protein s using arrows to represent beta sheets and helical lines for alpha helices see Figure 34 Figure 34 Cartoon graphics style If the Tube graphics style is used the backbone is visualized as a spline a piecewise parametric polynomial curve interpolating the positions of the alpha carbons in the backbone see Figure 35 molegro virtual docker user manual 3 User Interface page 44 251 Figure 35 An example of a protein backbone using the Tube graphics style The Difference Tube graphics style requires two superimposed protein chains to be present in the workspace The radius of the difference tube will be proportional to the distance between a C alpha atom from the selected protein chain and the nearest C alpha atom of any other chain in the workspace i e the C alpha atoms compared are not based on a sequence alignment This makes it possible to visualize where two superimposed structures differs the most It is also possible to set the color scheme for the backbone
83. a ligand deeply buried inside a macromolecule Far lo J Near 60 I Figure 22 Clipping Planes dockable window Clipping Planes can be enabled by choosing Window Clipping Planes from the menu bar Clipping Planes are enabled when the Clipping Planes window is shown and disabled when it is closed Adjust the near and far slider until the desired region is shown In MVD a Search Space is defined by a position x y z and a radius The search space is mainly used to define the volume a docking simulation explores but may be used for other purposes as well for instance cropping molecules in the workspace making a partial molecular surface or hiding molecules outside the search space The Search Space button on the main GUI toolbar makes it easy to toggle the search space on and off Toggling the Search Space button is identical to using the checkbox for the search space item in the Workspace s Constraints category with one exception if there is no search space in the workspace pressing the Search Space button will invoke the Search Space Setup dialog molegro virtual docker user manual 3 User Interface page 33 251 Search Space Setup i E a Mme Center Coordinates x jY 15 95 Set center of workspace Radius A Figure 23 Search Space Setup Dialog The Search Space Dialog makes it possible to set the center and the radius of the search space It is possible to directly set the center coordin
84. aced or not First the interaction energy between all ligand atoms and the water molecule is calculated using the PLP potential Ewater ligana Afterwards the water molecule is categorized into one of the following categories a Ignored a water molecule with no net ligand interaction Evwater ligand 0 is simply ignored water molecules located more than 6 angstrom from the ligand will not interact with the ligand a Displaced a water molecule is displaced if Ewater ligand gt Eremove water a Non displaced a water molecule is not displaced if Ewater ligand Eremove water g water molecules with favorable ligand interactions Ewater tigand lt 0 are always kept Using the displaceable water model the total energy contribution can be summarized in the following formula E Total water energy _ E Non displaced waters water ligand gt E water protein cofactor E water other waters E entropy reward Displaced waters Docking with displaceable water molecules can be enabled from the Docking Wizard or from MVD scripts If the Docking Wizard is invoked and the workspace contains one or more water molecules the option to setup displaceable water evaluation becomes available in the scoring function tab page To include displaceable water evaluation toggle on the Dispaceable Water option It is also possible to specify an entropy reward for displacing water molecules which adds a constant rewa
85. ads to feed one or more GPU s when doing GPU docking this is mainly the case for fast GPU s It is even possible to use multiple GPU s check the number of available GPU s in Help Show Available CUDA Devices The best way to find the optimal CPU GPU setting is by trying out different configurations on a sample test set of compounds but usually the best setting is to match the number of CPU processes with the number of physical cores and the number of GPU s with the available GPU s When docking in multiple processes a different progress dialog is displayed molegro virtual docker user manual 6 Docking Functionality Multiple Processes Docking Batchjob started ti 2 okt 12 45 09 2012 Hapsed 00 00 22 Finish estimated 12 45 32 Remaining 00 00 00 Working path C Users Mikael Documents MVD Data DockingOutput 245 eens EEE 100 0 100 12 45 09 365 12 45 09 367 12 45 09 369 12 45 30 442 12 45 32 188 12 45 32 515 12 45 33 170 12 45 33 170 12 45 33 170 12 45 33 172 Description Process spawned f SUBVERSION CHECKOUT Proje Process spawned f SUBVERSION CHECKOUT Proje Process spawned f SUBVERSION CHECKOUT Proje Process 1 completed Process 3 completed Process 2 completed Process 4 completed All processes done Wrote 40 result files Combining results C Users Mikael Documents MVD to file C Users Mikael Documents MVD Data Dock
86. ake the system slow to work with The data source wizard that appears is identical to the one described under Specifying a data source in the Docking Wizard molegro virtual docker user manual 5 Data Sources page 85 251 The Dock command will take a data source as input if it is surrounded by square brackets DOCK File C Molecules steroids sdf or DOCK Dir C Molecules Pattern sdf mol2 Index 10 100 Notice that all preparation of the data source will be performed according to the settings defined by any previous PREPARE and PARSERSETTINGS statements in the script E g PARSERSETTINGS breakUnrealisticBonds false combineMoleculeFragments tru PREPARE bonds ifmissing bondorders ifmissing hydrogens ifmissing charges always torsiontrees always detectcofactors false DOCK File C Molecules steroids sdf molegro virtual docker user manual 6 Docking Functionality 6 1 Cavity Prediction Potential binding sites also referred to as cavities or active sites can be identified using the built in cavity detection algorithm see Appendix IV Cavity Prediction for details General settings Molecular surface Expanded Van der Waals Max number of cavities 5 E Restrict to search space E Cofactors 2 2 E Proteins 2 2 w O Ligands 0 1 Figure 61 Cavity Prediction dialog A dialog is ava
87. al 21 Appendix IV Cavity Prediction In order to determine the potential binding sites a grid based cavity prediction algorithm has been developed The cavity prediction algorithm works as follows First a discrete grid with a resolution of 0 8 A covering the protein is created At every grid point a sphere of radius 1 4 A is placed It is checked whether this sphere will overlap with any of the spheres determined by the Van der Waals radii of the protein atoms Grid points where the probe clashes with the protein atom spheres will be referred to as part of the inaccessible volume all other points are referred to as accessible Second each accessible grid point is checked for whether it is part of a cavity or not using the following procedure From the current grid point a random direction is chosen and this direction and the opposite direction is followed until the grid boundaries are hit checking if an inaccessible grid point is hit on the way This is repeated a number of times and if the percentage of lines hitting an inaccessible volume is larger than a given threshold the point is marked as being part of a cavity By default 16 different directions are tested and a grid point is assumed part of a cavity if 12 or more of these lines hit an inaccessible volume The threshold can be tuned according to how enclosed the found cavities should be A value of 0 would only be possible far from the protein as opposed to a value of 100
88. and no reference ligand is specified the center of the bounding box spanning all protein s will be used The actual center of the binding site used is listed in the X Y and Z boxes in the window Besides the center of the binding site a Radius can be specified default is 15 angstrom The Search Space region will be shown in the Workspace Explorer in the Constraints category Notice A sphere in the Visualizer Window indicates the position and size of the current search space region see Figure 66 Figure 66 Example of search space region green sphere molegro virtual docker user manual 6 Docking Functionality page 95 251 Enable or Disable Additional Constraints If constraints besides the search space region have been added to the workspace they can be toggled on and off in the Enable or Disable Additional Constraints tab see Figure 67 In order for a constraint to be meaningful it must be defined within the current search space region rs Enable or Disable Additional Constraints Constraints Distance Constraint Type By ID Hard Ligand Atom Penalty Constraint on ID s 4 if more than one hard constraint is enabled during docking the docking engine will only attempt to satisfy one All enabled soft constraints will be used Please ensure that all constraints are inside the search space Figure 67 Enabling or disabling user defined constraints Choose Search Algorithm
89. around 1600 GFLOPS However GPU s are less flexible than conventional desktop CPU s which means the software must target GPU s specifically in order to utilize their computational power Molegro Virtual Docker offers a special mode for doing docking calculations using the GPU Since the algorithms had to be adapted to GPU the approach for GPU Screening is slightly different than the other algorithms in MVD The algorithm is described in The GPU Screening Algorithm The implementation in Molegro Virtual Docker is done using Nvidia s CUDA platform for GPU programming This means a CUDA capable graphics card from Nvidia is required to use the GPU screening modes There is no direct requirement on the computational power for the graphics card but it should be able to deliver more than 100 GFLOPS of computational power in order to make it preferable to use GPU s instead of CPU s Notice that our GPU implementation does not rely on double precision floating point support on the GPU This means that it is not necessary to use the Nvidia Tesla series hardware for doing scientific calculations The GPU screening can be performed on standard graphics hardware such as the Nvidia s GeForce or Quadro series of graphics cards Some machines may have more than one CUDA device installed for instance two graphics cards or a primary graphics card and a Nvidia Tesla card for scientific computations One instance of Molegro Virtual Docker will only be ab
90. as been prepared beforehand and saved in a format capable of handling all structural information e g Mol2 file format you should import it via the default preparation setting If Missing This setting only performs a given preparation if the required information cannot be found in the file Notice Per default any charge information for a molecule is ignored Assign charges Always means that MVD s internal charge scheme is always used to calculate charges If you want to use partial charges stored with the molecule set Assign charges If Missing this way MVD will only calculate charges for molecules with no charge information present If charges are imported from molecules e g provided with Mol2 files partial charges assigned to hydrogens will be moved to bonded heavy atom since explicit hydrogens are not taken into account by the scoring functions used during docking Inspecting the Warnings The last tab in the import dialog Warnings 0 shows potential problems with the structure file In this case no warnings are reported molegro virtual docker user manual 2 Docking Tutorial page 14 251 Now click the Import button The protein and the ligand appears in the Visualization Window see Figure 4 lg E Thvrmvdml Molegro Virtual Docker File Edit View Rendering Preparation Docking Tools Window Help e a Q i 4 v v Hydrogens Fog Hide Residues Search items Opt
91. as been re evaluated with the displaceable water option toggled on a Displaceable Water tab will be available see Figure 93 The Displaceable Water tab shows the following information about all water molecules available in the workspace ID Molecule ID also shown in Properties Window a Type ignored Displaced or Non Displaced Indicates whether a water molecule is ignored no interactions with ligand displaced because of non favorable interactions or non displaced favorable interactions with ligand a Detailed energy terms Energy contribution Energy water ligand Energy water protein cofactor Energy water other waters From the Options check box it is possible to focus on displaced and non displaced water molecules using the Hide Ignored Waters option or show all water molecules using the Show All Waters option From the list it is possible to visually inspect the water molecules in the 3D visualization window By clicking on one or more entries in the list the molegro virtual docker user manual 9 Displaceable Water page 145 251 corresponding water molecule is selected highlighted in the 3D visualization window if water molecules are toggled on in the Workspace Explorer window The Clear Selection button can be used to clear all current selections The total energy contribution from the displaceable water interactions is the sum of all values in the Energy contribution column This term named
92. ates of the search space or to place the center on either a The center of the proteins in the workspace a The center of a ligand or a pose in the workspace only the first 10 molecules in each category are shown a The center of a cavity only the 10 largest cavities are shown The center of all selected objects The Search Space Setup dialog may also be invoked from the application menu using Preparation Search Space Setup by using the context menu on the the search space item in the Workspace Explorer s Constraints category or by using the context menu on any atom or selection in the 3D view and selecting Set as center of search space The Hide Residues dialog can be invoked by pressing the Hide Residues button in the MVD Toolbar In order to show all protein residues again select the Hide Residues button on the MVD Toolbar The Hide Residues dialog see Figure 24 allows you to hide non relevant residues and molecules It is also possible to only display specific residue types It is possible to hide objects based on their distance to one of the following objects any ligand or pose in the workspace only the first twenty are listed any cavity any selected objects a search space or marked residues when using the Protein Preparation dialog If a ligand is chosen the minimum distance between all atoms in the ligand and all atoms in a given residue is calculated This residue is then hidden if it is farther away than t
93. ath mvd download complex complex pdb download from pdb org mvd importFrom Al1l complex pdb import into workspace mvd rmsd ligand 0 set a ligand as a rmsd reference mvd dock start the docking mvd exit Notice for Windows Users In order to use the Python wrapper you must install the Python for Windows extensions which can be downloaded from http sourceforge net project showfiles php group id 78018 Notice that you must download the version which targets your specific Python version Also notice that in order to communicate through pipes with the MVD application be sure to instantiate with a reference to the MVDConsole exe instead of the standard MVD exe application Use mvd MvdWrapper MvdWrapper C Program Files Molegro MVD Bin MVDConsole exe instead Of mvd Mvdwrapper MvdWrapper C Program Files Molegro MVD Bin MVD exe molegro virtual docker user manual 18 Appendix MolDock Scoring Function The MolDock scoring function MolDock Score used by MVD is derived from the PLP scoring functions originally proposed by Gehlhaar et al GEHLHAAR 1995 1998 and later extended by Yang et al YANG 2004 The MolDock scoring function further improves these scoring functions with a new hydrogen bonding term and new charge schemes The docking scoring function Escore iS defined by the following energy terms score inter intra where Enter is the ligand protein interac
94. avity is too small to be detected This situation makes it more difficult for the docking engine to identify the correct binding modes Constraints are limitations imposed on the molecular system based on chemical insight or knowledge Constraints can dramatically increase docking accuracy and speed as they often limit the search space considerably There are two fundamental kinds of constraints a Hard Constraints The docking engine tries to fully satisfy these constraints i e a hard constraint could be used to force a specific ligand atom to be in a given region The docking engine will enforce these constraints by moving or modifying the poses during docking If several hard constraints exist and none of them are satisfied the system will choose to satisfy an arbitrary one Notice that this means that not necessarily all hard constraints are satisfied If a hard constraint is not satisfied it will add 100 units to the soft constraint energy penalty a Soft Constraints These act as extra energy terms and contribute to the overall energy of the system As such they can be more or less satisfied They can for example be used to reward ligands in certain regions If several enabled soft constraints exist in the workspace they are ALL taken into account i e several extra terms are added to the overall docking energy function while docking molegro virtual docker user manual 6 Docking Functionality page 88 251 Creating Co
95. avoid overfitting and chance correlation in the subsequent data processing a Based on chemical reasoning The descriptors are based on properties which are believed to be chemically important not on abstract graph teoretical measures The descriptors are calculated using the following method molegro virtual docker user manual 14 Molecular Descriptor Calculations page 176 251 S Settings for CFDM Descriptor E Steric ALL Hydrogen Donors HD 7 Hydrogen Acceptors HA V Positively charged POS 4 Negatively charged NEG 7 Rings RING Charge threshold 0 2 f Reset All to Defaults Apply Figure 113 The CFDM descriptors can be configured by pressing the Configure button and choosing the tab Chemical Features in the Descriptor Calculation Wizard First all heavy atoms in the molecule are classified in one or more of the following chemical classes Steric All atoms belong to this class By default this class is not included in the CFDM calculation HD All atoms with hydrogen donor capabilities HA All atoms with hydrogen acceptor capabilities POS All atoms with a positive charge greater than the specified threshold default 0 2 NEG All atoms with a negative charge lesser than the specified threshold default 0 2 RING All atoms which are part of a ring system Then the topological distances between every pair of atoms are calcu
96. ble lt filename gt nogui interactive currentPath cudadevice lt ID gt licensedir macro lt label gt The lt filename gt parameter can be used to import molecular files during MVD startup If more than one file is listed separated by spaces each file will be imported Example Molegro MVD bin mvd 1stp pdb molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 164 251 If the filename has mvdscript as file extension e g mydocking mvdscript a script parsing progress dialog will be invoked and the script will be parsed and interpreted The nogui parameter can be used to run the script job without invoking the progress dialog Example Molegro MVD bin mvd mydocking mvdscript nogui Using the interactive parameter MVD can be started in interactive mode which is used to allow scripting languages e g Python to interact with MVD and control the docking process See Chapter 17 for more details The currentPath parameter can be used to override the working directory specified in the general preference settings with the current path This is particularly useful when running MVD from different working directories using a terminal window or when using a Script to start up MVD Example Molegro MVD bin mvd currentPath The cudadevice lt ID gt parameter can be used to specify the CUDA device ID from the command line Example Molegro MVD bin mvd cudadevice 0 The
97. bonding term and new charge schemes The docking scoring function Epiantsscore is defined by the following energy terms E j niseor J pip T f clash T f wT C site 20 where frp is a piecewise linear potential taking into account protein ligand interactions The PLP potential is similar to the one used by MolDock Score but here more interaction types repulsive buried nonpolar hydrogen bonding and metal are taken into account whereas MolDock Score only has two one for steric interactions and one for hydrogen bonding interactions The PLP interaction parameters used by MVD are Wpp hb 2 Wpip met 4 Wpip bur 0 05 Wpip nonp 0 4 Woip rep 0 5 Wiors 1 see KORB 2009 for details The ligand clash and torsional potentials faasa and fiors take into account internal ligand clashes and torsional contributions for the flexible bonds in the ligand see KORB 2009 for specific implementation details The Csite term specifies a penalty that is calculated if a ligand conformation pose is located outside the binding site defined by the search space sphere For each heavy atom located outside the binding site a constant value of 50 is added to the Cc term In addition a quadratic penalty is added if the ligands reference point i e the origin of the ligand s coordinate system is located outside the search space sphere KORB 2009 The 20 energy offset was originally needed for the PLANTS search algorithm molegro
98. cale since text is drawn differently by the raytracing engine text may appear either too large or too small This can be adjusted using the font scale settings Adaptive antialias is a technique for reducing jarred boundaries between objects Higher settings produce higher quality but takes longer time to render molegro virtual docker user manual 3 User Interface page 58 251 Save as Bitmap Figure 46 The output preview window After the output has been rendered a preview window appears with the result and the output can be saved as a bitmap The PNG format produces the highest quality images since it uses loss less compression while the JPG format produces the smallest file sizes 3 24 Biomolecule Generator Some PDB files contain transformation information for generating biomolecules To apply these transformations invoke the Biomolecule Generator by choosing Tools Biomolecule Generator molegro virtual docker user manual 3 User Interface page 59 251 REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THI REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSF REMARK 350 GIVEN BELOW BOTH NON CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN REMARK 350 REMARK 350 BIOMOLECULE 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT MONOMERIC REMARK 350 APPL
99. ccess to commonly used actions such as import of molecules docking using the Docking Wizard and pose inspection using the Pose Organizer Import Molecules Fitto Screen Screen Capture G i Q aw ig Hydrogens v Fog Hide Residues Search Space Ligand Map Energy Map Search v Label Dialog Toggle Hydrogens On Off Visualization Settings Figure 17 MVD Toolbar The MVD Toolbar also contains different toggle buttons The Hydrogens button makes it easy to switch between different view modes Show all hydrogens Show only polar hydrogens and Hide all hydrogens The Fog button is used to toggle fog effects on and off The Hide Residues button is used to toggle whether residues should be hidden or not see Section 3 9 for Docking Wizard molegro virtual docker user manual 3 User Interface page 26 251 more details The Search Space button makes it possible to define and toggle Search Spaces on and off see Chapter 3 8 and the Ligand Map button is used to toggle on 2D visualization of a ligand or pose and its interactions with the protein see Section 7 4 for more details Finally the Energy Map button visualizes the force field generated by the proteins in the workspace see Chapter 3 29 The Workspace Finder located at the far right side of the toolbar can be used to quickly search for molecule names and residue atom IDs see Section 3 10 for more details The Workspace Explorer window see Figur
100. ce page 63 251 3 strokes as the Title of the macro Similarly separators can be created between macro folders Again just use as the Title of the macro folder Macros can also be rearranged e g changing the order of occurrence within a macro folder or moving macros between folders by dragging and dropping a macro or a macro folder in the Macro overview listview If some macros are deleted or modified by mistake the default macro settings can be restored by pressing the Restore Macro Settings link located in the lower left corner of the dialog Alternatively the macros xml file can be replaced by a backed up version containing the default settings macros backup Both files are located in the Data directory The actual commands that can be used to define the macros are described in Appendix X Console and Macro Commands When importing molecules from PDB or SDF files header and annotation information is stored as part of the current workspace For PDB files the header is stored For SDF files the first 4 lines and any annotations are stored Imported notes can be shown using the context menu on any molecule in the Workspace Explorer or by selecting a molecule in the Workspace Explorer and pressing the Show PDB Header or the Show SDF Header button for PDB and SDF files respectively PDB File Header 3ptb_1 pdb PDB File Header 3ptb_1 pdb HEADER HYDROLASE SERINE PROTEINASE 27 SEP 82 3PIB TITLE THE GEOMETRY OF THE
101. ceicrtis sive ciasiwiadiviwends havadiieessvieeadeueades 154 10 4 Inspecting RESUS sccscncceeecav sae naesiediachechads a a a ERS 155 11 Customizing Molegro Virtual Docker ssssssssssssrrssrrssrrerrrrerrrerresrrrnn 157 11 1 General PreferenceS sssssrrsssrsnrsssrnnosssnnnrosannnrronsannrrrsennnrnsnenans 157 11 2 Command Line Parameters ccccccceeeee eee eseeeeeeeeeeenenssseeensneeees 163 11 3 Changing Re ranking Score Coefficients ccc cccseeeee eres eeeeaeeeneees 164 12 Obtaining the Best Docking ReSUItS cccccccceeeeeee eee eeeeseeeeeeenneneeees 165 12 1 Preparauonicisssieccsahimrnsmscncotantnehouteladenlelanguivianmnononiaasimabats 165 12 2 DOCK INO rias dus ven ces nw ints else dows ewdeua tex ssiiawe A EA 166 12 3 Post analySiS usssssssnnnnnsssrnnnnsarnnnnnnasnrnnnnunnrsrunnnnsnnnnnnnenannnnnnn 167 13 Molegro Data Modeller Integration ss ssssssssrsrsrrrssrssrrnnrrrsrrrerressrenn 168 molegro virtual docker user manual page 5 251 14 Molecular Descriptor Calculations cceccceeee eee ee eee eee eeeeeeenaneeennanees 170 14 1 Using the Descriptor Calculation Wizard ss ssssssssssssressrrrsrrssrens 170 14 2 DESChIPtOrs M MVD iscscriccnnconnte mira hebatinnianerndencr sins mes EE EES EE EA 171 14 3 Choosing an Output FOMMabsiec lest uenielianbolaictesintoncaceiabeucsnesieesies 174 14 4 Working with Molecular DescriptorS ssssssssssssrsssrrsrrrsrrinsressrersns 174 14 5 Chem
102. cid eter DecseeieGesiarseedapsse 225 28 1 List of Script Commands Available cccccccceeeee eee eeeeeeeennaeenenaaes 226 28 2 PIOW CONT Olas iva sisikian vmciend twat behienabnrhesieninreteaminwicesdeneihiva 241 29 Appendix AIT MOIDOCK SEysseses sezecadisetsenesnvecepasedees ew ieee leew a E 243 30 Appendix XIII Iterated SIMpPlex cc ccccece eee seseeeeeeeeeeeeesseeseeeeeneneees 246 31 Appendix XIV Grid based SCOPesS cccsecseeeseeeeeesseeeeesseeeeeeeeensnaeees 248 molegro virtual docker user manual page 6 251 32 Appendix XVI RETEPENCES 6s sicciccviscceseiatsesreascesavaererieieecsseiedewsatecansaw 250 molegro virtual docker user manual 1 Introduction to Molegro Virtual Docker Molegro Virtual Docker MVD is an integrated environment for studying and predicting how ligands interact with macromolecules The identification of ligand binding modes is done by iteratively evaluating a number of candidate solutions ligand conformations and estimating the energy of their interactions with the macromolecule The highest scoring solutions are returned for further analysis MVD requires a three dimensional structure of both protein and ligand usually derived from X ray NMR experiments or homology modeling MVD performs flexible ligand docking so the optimal geometry of the ligand will be determined during the docking The preferred way to get started with MVD is a Read the remainder of the introdu
103. cific search algorithm parameters are set by the OPTIMIZER script command see Appendix XI Script Commands for more details molegro virtual docker user manual 31 Appendix XIV Grid based Scores MolDock Score Grid and PLANTS Score Grid are grid based versions of the MolDock Score and Plants Score functions respectively The grid based scoring functions precalculate potential energy values on an evenly spaced cubic grid in order to speed up calculations The energy potential is evaluated by using tri linear interpolation between relevant grid points The rest of the terms in the Grid based versions i e internal ligand energy contributions and constraint penalties are identical to the standard version of the scoring functions Notice that unlike the standard MolDock Score the grid version of MolDock Score does not take hydrogen bond directionality into account hydrogen bonding is determined solely on distance and hydrogen bonding capabilities Grids are not stored permanently they are calculated when needed Grid generation is relatively fast Typically 15 seconds for the standard settings Grids will automatically be reused while running docking scripts as long as the target protein does not change Notice that large energy grids with high resolution can consume a lot of memory Grid resolutions of 0 3 0 4 A will be adequate in most cases Look out for the estimated memory usage in the Docking Wizard As a rul
104. cker using Tools Molegro Data Modeller There are also short cuts for viewing data in Molegro Data Modeller when working with the Pose Organizer see page 111 Molecular Descriptors see page 174 and when doing advanced template regression models see page 153 Molegro Data Modeller can be used for Regression Multiple Linear Regression Partial Least Squares Support Vector Machines and Neural Networks Classification K Nearest Neighbors and Support Vector Machines Chemistry 2D depictions in spreadsheets and plots SDF and SMILES support Feature selection and cross validation is simple to set up and use using built in wizards Automated fine tuning of regression model parameters using grid based search Principal Component Analysis PCA Visualization Histograms 2D scatter plots 3D plots and Spring Mass Maps Clustering K means clustering and density based clustering Outlier Detection Similarity Browser molegro virtual docker user manual 13 Molegro Data Modeller Integration page 169 251 Sophisticated subset creation create diverse subsets by sampling from n dimensional grids lk Molegro Data Modeller MoleculeDepiction mdm Bie Edit Preparation Modelling Visualization Window Modules Help ESA lB Stl E E i P selection Descriptors Al Coloring By descriptor gt f Workspace Explorer x Name TH c N o P S Other items E Workspace Molecule Depiction f Molecule Depiction Datasets 1 Li
105. click and selecting Set as Rotational Center Another option is to choose Fit to Screen from the Workspace Explorer context menu Fit to Screen will set the rotational center to the center of the bounding box enclosing the chosen molecule If Fit to Screen is invoked from the MVD Toolbar or from the Visualization Window context menu the new rotational center will be the center of the bounding box enclosing all visible molecules in the Visualization Window Manipulating Visualization Objects All objects in the 3D world have context menu actions These can be used for changing their properties e g setting hybridization partial charge implicit hydrogens or hydrogen bond types for atoms and bond order or bond flexibility for bonds See Section 4 3 for more details ys 3 6 Console Window The Console Window at the bottom of the screen displays information warnings and errors The input field at the bottom of the console window molegro virtual docker user manual 3 User Interface page 32 251 allows the user to enter console commands The amount of information in the console can be controlled with the associated context menu right mouse button click e g info warnings and debug messages can be turned off Clipping Planes allows you to change the clipping planes of the visualization window i e how close and how far away objects are drawn This can for example be useful if you want to visualize the interior of a protein or
106. corresponding to a binding site buried deeply in the protein The final step is to determine the connected regions Two grid points are connected if they are neighbours Regions with a volume below 10 0 A are discarded as irrelevant the volume of a connected set of grid points is estimated as the number of grid point times the volume of a unit grid cell The cavities found are then ranked according to their volume molegro virtual docker user manual 22 Appendix V Clustering Algorithm The multiple poses returned from a docking run are identified using the following procedure During the docking run new candidate solutions poses scoring better than parental solutions see Appendix III MolDock Optimizer for details are added to a temporary pool of docking solutions If the number of poses in the pool is higher than 300 a clustering algorithm is used to cluster all the solutions in the pool see below The clustering is performed on line during the docking search and when the docking run terminates Because of the limit of 300 poses the clustering process is fast The members of the pool are replaced by the new cluster representatives found limited by the Max number of poses returned option The clustering procedure works as follows 1 The pool of solutions is sorted according to energy scores starting with the best scoring pose 2 The first member of the sorted pool of solutions is added to the first initia
107. creen Toggle dockable windows Toggle Cofactors category on off Toggle Ligands category on off Toggle Proteins category on off Toggle Water category on off Quit MVD Invoke misc visualization views Invoke misc dialogs Notice Some of the shortcuts can be modified from the Macro and Menu Editor and additional shortcuts can be defined for macro commands molegro virtual docker user manual 2 Appendix X Console and Macro Commands When using the Macro and Menu Editor or entering commands in the console the following commands can be used Notice Some commands require a molecule target these can be described using the following syntax Ligand O the ligand with ID 0 Ligand 4 5 6 the Ligands with IDs 4 5 and 6 Multiple IDs are separated by comma Ligands All ligands By using the plural form of a category all molecules in it are selected The categories are Pose Cofactor Protein Water Ligand Poses Cofactors Proteins Ligands Water 0 All Poses Cofactors Proteins Ligands and the first Water molecule Multiple targets can be concatenated using a semi colon Notice The IDs of molecules are based on the order of occurrence in the corresponding Workspace Explorer category For instance ligand molecules listed in the Ligands category begins with index 0 with increments of 1 i e 0 1 2 3 If molecules are removed from the workspace the IDs of the molecules are changed to follow the new order of oc
108. ction Chapter 1 m Go through the docking tutorial Chapter 2 a Read the instructions on how to use the GUI Chapter 3 Overall Chapters 3 to 9 describe various aspects of MVD from importing and preparing molecules to docking and inspecting the docked solutions Chapter 8 describes docking with flexible sidechains Chapter 13 describes the Molegro Data Modeller integration which makes it possible to perform advanced data visualization and modelling Chapter 17 provides an overview of the scripting features in MVD More detailed information about the algorithms cavity detection clustering binding mode prediction and scoring functions MolDock Score and PLANTS Score used by MVD can be found in the appendices molegro virtual docker user manual 1 Introduction to Molegro Virtual Docker page 8 251 Molegro Virtual Docker is developed by CLC bio a Qiagen company Silkeborgvej 2 Prismet 8000 Aarhus Denmark http www cicbio com VAT no DK 28 30 50 87 Telephone 45 70 22 55 09 Fax 45 70 22 55 19 E mail info clcbio com If you have questions or comments regarding the program you are welcome to contact our support function E mail support clicbio com The system requirements for Molegro Virtual Docker are a Windows 7 Vista 2003 XP or 2000 a Linux Linux The officially supported system is Ubuntu 12 04 LTS We provide both 32 and 64 bit builds Please send a mail to support clcbio com if you experience p
109. currence in the list molegro virtual docker user manual 27 Appendix X Console and Macro Commands page 221 251 Command Description Export as Mol2 or PDB A File export dialog is opened for EXPORT moleculetarget See of a filename i p SURFACEDIALOG Shows the Surface dialog PREPAREDIALOG Shows the Preparation wizard DISTANCECONSTRAINT Shows the Distance constraint dialog LABELDIALOG Shows the Label dialog DOCKINGWIZARD Shows the Docking Wizard Downloads PDB with key 4 letter code from the GETEDE key Protein Data Bank ALIGN MoleculeTarget1 id1 id2 id3 MoleculeTarget2 id1 id2 id3 Aligns atom id1 id2 id3 in MoleculeTarget1 with atom id1 id2 id3 in MoleculeTarget2 SHOW CATEGORY lt category gt Shows or hides Workspace Explorer category with given name HIDE CATEGORY lt category gt i e SHOW CATEGORY water CD Print current directory DIR Shows dir of MVDML files in current directory MKDIR lt directory gt Make a new directory named directory RM lt directory gt Remove directory named directory PREV Loads previous MVDML file in current directory NEXT Loads next MVDML file in current directory RMSD Invokes RMSD dialog CAV Invokes Cavity detection dialog Selection of objects SELECT ID lt id gt SELECT ATOM lt x y z gt SELECT RESIDUE lt id gt SELECT RESIDUEID lt id gt SELECT ID selects all atoms
110. d Hydrogen bonds no directionality NoHBond90 Electrostatic short range Electro Electrostatic long range ElectroLong Cofactor Ligand E Inter cofactor ligand Steric by PLP Not present in the mvdresults file but can be calculated as E Inter cofactor ligand Cofactor hbond Cofactor elec Steric by LJ12 6 Cofactor VdW molegro virtual docker user manual 7 Analyzing the Docking Results page 124 251 Hydrogen bonds Cofactor hbond Electrostatic Cofactor elec Water Ligand interactions E Inter water ligand Displacable Water interactions E DisplacedWater Internal Ligand interactions E Intra tors ligand atoms Torsional strain E Intra tors Torsional strain sp2 sp2 E Intra sp2 sp2 Hydrogen bonds E Intra hbond Steric by PLP E Intra steric Steric by LJ12 6 E Intra vdw Electrostatic E Intra elec Search Space Penalty E Penal Soft Constraint Penalty E Soft Constraint Penalty molegro virtual docker user manual 7 Analyzing the Docking Results page 125 251 On the settings tab the ligand evaluation can be customized This can be important when inspecting poses from a docking run Since the Ligand Energy Inspector is not aware of which scoring function settings were used during the docking it is necessary to match the settings here to those selected in t
111. d binding site Now we are ready to start the docking To get a clearer view of this process start by selecting View Reset View This will reset the 3D view and hide the surface Now select View Docking View This will switch to a view where ligands and poses have different colors and capped stick representation instead of ball and stick The Docking Wizard is invoked by selecting Docking Docking Wizard The first tab shows which structures are included in the simulation If multiple ligands are available they can be chosen here Since we are doing a redocking study here we will use the only available ligand as reference Set Reference Ligand to XK2_263 and continue to the next tab by pressing Next The most important thing on the next tab is to set the binding site Since we have detected cavities we set Origin to Cavity 1 If the protein had multiple potential binding sites more choices would appear see Figure 9 Binding Site Origin Reference Ligand Center X 9 21 Rome 5 E Figure 9 Selecting the binding site molegro virtual docker user manual 2 Docking Tutorial page 18 251 Now continue to the next tab where Search Parameters can be set We will not change any search parameters press the Next button to proceed to the next tab The next tab Pose Clustering allows you to configure whether multiple poses should be returned We will stick to the default setting which will limit the numb
112. d job will create one MVD results file and a number of poses for each job unit molegro virtual docker user manual 15 Molegro Virtual Grid page 188 251 f Combine Results Combine the results from 6 MVD results files Output filename combined mvdresults V Limit the number of poses a Maximum count 1000 5 Filter by values in RerankScore x column Figure 119 The interface for combining results Even though MVD is able to import multiple MVD results files at the same time using the Pose Organizer larger jobs quickly become difficult to handle this way Therefore the controller is able to combine multiple MVD results files into a single file For larger runs gt 1000 ligands it is also possible to filter the combined results before importing them into the Pose Organizer This is done by enabling Limit the number of poses and choosing a desired number of poses Normally the best choice would be to filter by lowest RerankScore or PoseEnergy but it is possible to choose between all terms available in the MVD results file Using filtering makes it possible to handle very large virtual screening runs When the combination and filtering has completed a new combined MVD results file is written to the chosen location It is possible to drag the yellow label directly onto the MVD GUI to inspect the poses with the Pose Organizer or manually import the results file in MVD As mentioned in the Licen
113. ded to cluster the returned poses see Section to lower the number of similar poses reported when taking all docking runs into account a Multiple poses It is advisable to return multiple poses for each docking run typically between 3 and 10 and rerank the poses found afterwards see Ranking poses bullet below m Check warnings The last tab in the Docking Wizard highlights potential warnings and errors It is important to inspect the warning messages and see if further actions are needed Otherwise the docking run might be unsuccessful a Ranking poses The most promising poses returned when the docking run terminates can be further analyzed in the Pose Organizer Ideally the highest scoring pose should represent the best found binding mode However this is not always the case A useful feature is to evaluate the poses using the Reranking Score The Reranking Score makes use of a more advanced scoring scheme than the docking scoring function used during the docking run Using the Reranking Score will often increase the accuracy of the ranked order of the poses molegro virtual docker user manual 13 Molegro Data Modeller Integration Molegro Data Modeller is a powerful tool for data mining data modelling and data visualization Since Molegro Virtual Docker 6 0 Molegro Data Modeller is available as an integrated standard component and replaces the previous Data Analyzer It can be launched from inside Molegro Virtual Do
114. dentified as the RSA Data Security Inc MD5 Message Digest Algorithm in all material mentioning or referencing this software or this function License is also granted to make and use derivative works provided that such works are identified as derived from the RSA Data Security Inc MD5 Message Digest Algorithm in all material mentioning or referencing the derived work RSA Data Security Inc makes no representations concerning either the merchantability of this software or the suitability of this software for any particular purpose It is provided as is without express or implied warranty of any kind These notices must be retained in any copies of any part of this documentation and or software molegro virtual docker user manual 25 Appendix VIII Third Party Copyrights page 218 251 Icons The icon set used in MVD is taken from The Tango Icon Library http tango freedesktop org Tango_Desktop_ Project They are released under the Creative Commons Share Alike license http creativecommons org licenses by sa 2 5 molegro virtual docker user manual 26 Appendix IX Keyboard Shortcuts The following list contains the keyboard shortcuts available in MVD On Mac OS X the CTRL key is replaced by the command key CTRL O CTRL SHIFT O CTRL SHIFT C CTRL S CTRL F CTRL H CTRL C CTRL L CTRL P CTRL W CTRL Q CTRL 1 to 8 F1 to F9 Import Molecules Open Workspace Clear Workspace Save Workspace Toggle full s
115. dified using the EVALUATOR and OPTIMIZER commands It is also possible to specify a Data Source using bracket syntax DOCK File molecules test sdf See the Data Source chapter for more information Notice that data source parser is able to read UTF 8 or UTF 16 Unicode encoded files It is also able to read 8 bit Local encoded files but will not parse special national characters correctly If errors are encountered with special characters for instance in the name of the ligands try converting the files to Unicode Examples DOCK Ligand 50 60 Docks ligand from number 50 to number 60 both included in the current workspace DOCK Ligand 0 Docks first ligand in the current workspace DOCK Ligands Docks ALL ligands in workspace molegro virtual docker user manual 28 Appendix XI Script Commands page 230 251 EVALUATOR lt initstring gt Sets the settings for the evaluator the docking score function There is normally no need to change these The lt initstring gt is semi colon separated string of parameter value pairs The following parameters are available Their default setting is marked in bold face General parameters available to MolDock Score and Plants Score cropdistance double Determines whether the protein should be cropped meaning protein atoms outside a given distance is not taken into account If crop distance is 0 the default settin
116. ding energy protein ligand as calculated if the directionality of the hbond was not taken into account Notice This term is not used by the MolDock score VdW LJ12 6 Protein steric interaction energy from a LJ 12 6 VdW potential approximation Notice This term is not used by the MolDock score molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 203 251 E Inter water ligand The MolDockScore interaction energy between the pose and the water molecules E Intra tors ligand atoms The total internal MolDockScore energy of the pose E Intra steric Steric self interaction energy for the pose calculated by PLP E Intra hbond Hydrogen bonding self interaction energy for the pose calculated by PLP Notice This is a non standard term and is zero by default it must be enabled by specifying the internalhbond true option to the EVALUATOR initializer list in a MVDScript file or by enabling the Internal HBond option in the Docking Wizard E Intra elec Electrostatic self interaction energy for the pose Notice This is a non standard term and is zero by default it must be enabled by specifying the ligandes true option to the EVALUATOR initializer list in a MVDScript file or by enabling the Internal ES option in the Docking Wizard E Intra tors Torsional energy for the pose E Intra sp2 sp2 Additional sp2 sp2 torsio
117. does not match any of the defined protonation states for the given residue These errors can be fixed by changing the protonation state into a valid state These residues are shown with yellow spheres in the 3D view On the protonation tab a list view displays all residues for the proteins in the workspace The green arrows jump to the next or previous erroneous residue either improper structure or unknown protonation state molegro virtual docker user manual 4 Preparation page 74 251 Protonation Mutate and Optimize Settings Ww Wamings 1 Action Select v Residue ID Choose Protonation a Asn 4 Val 75 Val 76 cu 7 CLU Gly 78 Asn 79 Glu 80 GLU Gin 81 Phe 82 le 83 Hide Residues This residue has a valid protonation a Atom GLU GLZ GLZ1 Figure 55 The Protein Preparation Dialog The lower panel displays the current protonation state If a residue has alternate protonation states they can be chosen in two different ways a By choosing a residue in the list view and then changing the state from the drop down menu in the third column Choose Protonation a By using the context menu in the 3D visualization view on a residue marked by a red or yellow sphere Because it can be difficult to get an overview of the individual residues it is possible to invoke the Hide Residues dialog directly from the protonation preparation dialog The Hide Residues button provides a sho
118. drogen bond strength Hacor D C a790 150 D n a aa 909 100 P d aaa 90 100 Here AA Acceptor Antecedent denotes a heavy atom connected to the acceptor A D denotes the donor and H is the donated hydrogen atom The ramp function is defined as D A Aminj Amax O for ASAmin and A Aminj Amax 1 for A Amax and is linearly interpolated between these values for Amin lt A lt Amax If it is not possible to calculate one of these factors it is omitted This is for example the case for hydroxy rotors where the exact location of the hydrogen is not investigated during docking and the two first factors cannot be calculated The angle checks above were motivated by the approach taken by McDonald and Thornton MCDONALD 1994 Eintra is the internal energy of the ligand E a E prp r Al cos m 0 E i ligand j ligand flexible bonds clash The double summation is between all atom pairs in the ligand excluding atom pairs which are connected by two bonds or less The second term is a torsional energy term parameterized according to the hybridization types of the bonded atoms see Table 6 is the torsional angle of the bond Notice that this angle is not necessarily uniquely determined The average of the torsional energy bond contribution was used if several torsions could be determined The last molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 201 251 term Eciash
119. e Limit the number of poses reported Max number of poses returned Only report poses with energies less than a user defined threshold Enable energy threshold Cluster poses using the specified RMSD threshold Cluster similar poses Poses found during the docking run will be clustered put into bins using the RMSD criteria See Appendix V Clustering Algorithm for a detailed description of the clustering algorithm used Only the lowest energy representative from each cluster will be returned when the docking run is completed Increasing the RMSD threshold will increase the diversity with respect to RMSD of the poses returned The Ignore similar poses option is used to avoid reporting to similar molegro virtual docker user manual 6 Docking Functionality page 98 251 poses when conducting multiple runs docking the same ligand All poses returned from the runs will be clustered and similar poses are removed keeping the best scoring one Depending on the RMSD threshold specified more or less diverse poses combined for all the runs will be reported Pose Clustering Multiple poses Retum multiple poses for each run Max number of poses retumed 5 Enable energy threshold 0 00 7 Cluster similar poses RMSD threshold 1 00 V Ignore similar poses for multiple runs only RMSD threshold 1 00 Retum one pose for each run Tabu clustering penalize poses similar to solutions from earlier runs MSD threshold
120. e 0 hydrogens 0 element C gt lt Atom pdbName N hyb 2 charge 0 hydrogens 1 element N gt lt Atom pdbName 0 hyb 2 charge 0 hydrogens 0 element 0 gt lt Atom pdbName 0D1 hyb 3 charge 0 5 hydrogens 0 element 0 gt lt Atom pdbName 0D2 hyb 2 charge 0 5 hydrogens 0 element 0 gt lt Bond from CA to N order 1 gt lt Bond from CA to CB order 1 gt lt Bond from CA to C order 1 gt lt Bond from C to 0 order 2 gt lt Bond from CB to CG order 1 gt lt Bond from CG to 0D2 order 2 gt lt Bond from CG to OD1 order 1 gt lt Protonation name ASZ pdbAlias ASZ1 description 0D2 protonated Neutral gt lt Atom pdbName 0D1 charge 0 hydrogens 0 gt lt Atom pdbName 0D2 charge 0 hydrogens 1 gt lt Protonation gt molegro virtual docker user manual 4 Preparation page 79 251 lt Protonation name ASZ1 pdbAlias ASZ21 description 0D1 protonated Neutral gt lt Atom pdbName 0D1 charge 0 hydrogens 1 gt lt Atom pdbName 0D2 charge 0 hydrogens 0 gt lt Protonation gt lt Residue gt lt Bond from CA to N order 1 gt lt Bond from CA to C order 1 gt lt Bond from C to 0 order 2 gt lt Residue gt lt ResidueDefinitions gt The residue template always consists of a base or default protonation which describes the atoms
121. e discarded and the original conformation will no longer be available Conformations are saved together with the workspace in the MVDML file format Notice that before saving the program will always change to default conformation and when loading workspaces the default conformation will always be the currently selected conformation at startup 3 22 Visualization Settings Dialog The graphical settings for the 3D visualization can be adjusted by selecting Rendering Visualization Settings Dialog Graphical Styles and Coloring Schemes Visualization Settings Style and Color Rendering Interactions Views Choose target Proteins Graphical style Ligands Wireframe Poses Water Line Width fel Cofactors Fast wireframe visualization Coloring Fixed Color Fixed color Restore to Default Settings Apply Cancel Figure 41 The Visualization Settings dialog molegro virtual docker user manual 3 User Interface page 51 251 From the Style and Color tab select a category from the list on the left side of the tab one of Proteins Ligands Poses Water and Cofactors and adjust either its graphical style or color scheme The following graphical styles can be chosen Ball and Stick Atoms are drawn as spheres balls and bonds are drawn as cylinders sticks The Atom Scale parameter sets the fraction of the Van der Waals radius that is used as radius for
122. e 0 9 keepmaxposes 5 Dock FOR SMVDML IN 3PTB 1HVR 1LIC 1TMN SMVDML will be replaced by the appropriate value in the loop LOAD C BENCHMARK SMVDML mvdml RMSD ligand 0 DOCK NEW ENDFOR This script can be used to divide the workload between different machines Init with appropriate settings first DOCKSETTINGS maxIterations 1000 runs 10 MaxPoses 5 EVALUATOR cropdistance 0 hbond90 true OPTIMIZER cavity true popsize 50 crossoverrate 0 9 keepmaxposes 5 For machine 1 LOAD C BENCHMARK 1HVR mvdml IMPORT LIGAND 0 99 FROM DB sdf DOCK For machine 2 LOAD C BENCHMARK 1HVR mvdml IMPORT LIGAND 100 199 FROM DB sdf DOCK MVD can also run in interactive mode molegro virtual docker user manual 17 Script Interface page 196 251 In this mode the MVD application starts and waits for user input from the command line i e it reads and writes from the standard input and output which can be piped To start MVD in interactive mode use the following syntax Example mvd interactive The purpose of the interactive mode is to allow scripting languages capable of writing to and from the standard input and output of a program to control the docking process This can be useful for automating larger docking runs When in interactive mode MVD will send an DONE lt command gt after each command has
123. e 18 contains information about the 3D objects both molecules such as proteins ligands and water molecules but also objects such as labels surfaces backbones and cavities Workspace Explorer tems Options Workspace New v Fit to screen co Constraints 1 Ligands 1 Hide others a Poses 10 00 BTN_300 01 BTN_300 02 BTN_300 03 BTN_300 04 BTN_300 05 BTN_300 06 BTN_300 07 BTN_300 08 BTN_300 09 BTN_300 Proteins 1 K EKEK K KK K K Figure 18 Workspace Explorer window The context menu right mouse button click allows the user to a Export molecules to PDB Mol2 or SDF format a Edit workspace properties workspace title and workspace notes a Rename molecules a Remove items from the current workspace a Set the currently active ligand a Set all torsions in a ligand either rigid or flexible a Copy ligands to poses used to inspect ligands with the Pose Organizer molegro virtual docker user manual 3 User Interface page 27 251 a Clone ligand or protein makes a copy of the molecule Convert ligand to pose or cofactor a Convert protein to ligand a Convert pose to ligand used when docking poses a Modify ligand or pose using the Pose Modifier a Detect cavities using the Cavity Prediction dialog and merge them Export cavity grid points to PDB or Mol2 format represented as water molecules a Inspect poses using the Pose Organizer a Prepar
124. e ai E KANAA 193 17 1 Using the Script Interface ssssssssssssrrrsrrrerrrsrrrrrrnrrrrerrrerrrnsrenna 193 17 2 Running a Text file Script s s sssrrnnnnuusrrrnnuunarrsunnnnnsrernnnnnannannnnn 193 17 3 Examples of Common Script JObS sssssssssssssrrrsssrrrrsesrrrrrrsrrrrrnns 194 17 4 Running the Script Interface Interactively sssssssssrsrrisrressrsssres 195 17 5 Running the Script Interface From Python cccceeeee essen eeeee eee eees 196 18 Appendix I MolDock Scoring FUNCTtION cccceeeee ee eens eeeeee eee eeeneannas 198 19 Appendix II PLANTS Scoring FUNCtiON ccccceceeeseeeseeeeenseeeeeneeeen ees 205 20 Appendix III MolDock OpPtiMiZeh ies seed scoesieacbewsewdiacobroseeteiecoveebsiasdwsededs 207 21 Appendix IV Cavity Predictions vi sscecoies ve idiswvscdensavevadveewesoenieeioneeiwadeeess 210 22 Appendix V Clustering AIQOrithm cccceescceeeeeseeeeeeeeeneseeeeenneentes 211 23 Appendix VI Supported File Formats ssssssssssssrrsssrrrrnssrrrrrssrrrrrrssse 213 24 Appendix VII Automatic Preparation ccccececeee esse eee eeeeeeeeneeeenaeenes 215 25 Appendix VIII Third Party COPVHiGNUS vic ce cess ct eewes ve eaaied eeeosesetroteedorevestas 217 26 Appendix IX Keyboard Shortcuts wis scscseviwiseccs vessacdvnstavedartaveeswiaweeewsaes 219 27 Appendix X Console and Macro COMMANGG ccceeeeeeeeeeeeeeeeeeeeeeeees 220 20 Appendix XI Script CommandS coccsessdevicvieineteie
125. e molecules Create labels surfaces and backbones a Fit the molecule to the visualization window The Workspace Explorer can also be used to inspect molecules in the Visualization Window using the left mouse button to select the molecules or by using keyboard shortcuts see below The Options button see Figure 18 contains settings used to customize the behavior when inspecting molecules The Fit to screen option will automatically zoom selected molecules so that they fit into the Visualization Window The Show hydrogen bonds option can be used to display hydrogen bonds only applicable for ligands and poses The Hide others option toggles whether other checked molecules in the current workspace category are allowed or not Keyboard shortcuts are also available for inspecting molecules Pressing the Shift button while clicking the left mouse button on a molecule in the chosen category e g Ligands or Poses will fit the selected molecule in the Visualization Window and all other molecules located in the same category are hidden Alternatively using Ctrl Shift when clicking on a molecule hydrogen bonds are shown for the selected molecule Instead of using the mouse to select molecules to inspect Up or Down keys can be used to browse the molecules present in the currently selected Workspace Explorer category If the Ctrl and Shift shortcuts are omitted the settings enabled in the Options panel will be used If multiple receptor co
126. e of thumb it should never exceed more than half of the physical memory available in the computer Also notice that if several instances processes of MVD is running each process will need to generate its own grid In order to use the MolDock Score grid version select it as the evaluation function in the Docking Wizard Scoring Function gt Score gt MolDock Score GRID molegro virtual docker user manual 31 Appendix XIV Grid based Scores page 249 251 In order to use the PLANTS Score grid version select it as the evaluation function in the Docking Wizard Scoring Function gt Score gt PLANTS Score GRID To use the grid based scoring function the EVALUATORTYPE script command has to be set Moreover specific grid parameters are set by the EVALUATOR script command see Appendix XI Script Commands for more details molegro virtual docker user manual 32 Appendix XVI References THOMSEN 2006 Thomsen R Christensen M H MolDock A New Technique for High Accuracy Molecular Docking J Med Chem 2006 49 11 3315 3321 CCG Chemical Computing Group www chemcomp com SCHRODINGER Schr dinger LLC www schrodinger com GEHLHAAR 1995 Gehlhaar D K Verkhivker G Rejto P A Fogel D B Fogel L J Freer S T Docking Conformationally Flexible Small Molecules Into a Protein Binding Site Through Evolutionary Programming Proceedings of the Fourth International Conference on Ev
127. e option The right panel shows the job units of the currently loaded job only one job can be loaded at a time Jobs created by the Docking Wizard are automatically loaded when the controller is started It is also possible to load jobs using the File Open Job dialog or by dragging a job description file onto the GUI When Start job is pressed the controller will begin dispatching units to the available agents The Remove job button removes the currently loaded job from the controller This action does not delete any files All results are still stored on the controller computer From the Job menu it is also possible to perform the Reset job action Resetting a job sets all units to the pending state All produced log files and results are deleted from disk and lost The following additional actions are available using either the context menu or the Job menu Show log file This will show a log file for the unit This includes any log messages produced by running MVD on the remote agent Retry unit Occasionally units fail This might be due to invalid molecule structures MVD settings or network transmission errors Since some types of errors such as invalid molecule structures can not be corrected the controller will not automatically retry a failed unit However it is possible to use the retry unit action to rerun the unit Notice that the job menu also contains an option for retrying all non completed units A distribute
128. e pose was created from Name The internal name of the pose a concatenation of the pose id and ligand name Filename The file containing the pose Workspace The workspace mvdml file containing the protein Notice This entry appears in the header of the mvdresults file Run When running multiple docking runs for each ligand this field contains the docking run number Energy terms molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 202 251 total Energy The MolDock score arbitrary units Notice that this value is always calculated using the non optimized MolDock score and hence may differ from the PoseEnergy below which may use interpolation on precalculated grids RerankScore The reranking score arbitrary units PoseEnergy The score actually assigned to the pose during the docking Notice that since the score is calculated by the scoring function chosen in the Docking Wizard there may be small differences to the MolDock score reported in the Energy entry for instance when using the grid based version of the MolDock score the grid interpolation may result in slighty different energies as compared to the non grid MolDock score version SimilarityScore Similarity Score if docking templates are enabled LE1 Ligand Efficiency 1 MolDock Score divided by Heavy Atoms count LE3 Ligand Efficiency 3 Rerank Score divided by Heavy Atoms
129. e regions correspond to a nearby positive charge in the protein The electrostatic potential is the sum of the Coulomb potentials for each atom in the protein with a distance dependent dielectric constant see Chapter 18 The electrostatic field is not used with the PLANTS Scoring function All the fields take the steric interaction into account so that only grid positions where it is possible to place an atom without steric clashes with the protein are shown For instance there may be charged regions inside the protein which are not shown because it is not possible to place a ligand atom there It is possible to adjust the appearance of the fields The Threshold slider determines at which point an interaction is strong enough to be included in the visualization A higher threshold value results in less points being shown The Dot Size determines how large the transparent blobs that make up the volumetric fields are The Transparency slider controls how opaque the fields appear Higher values make the fields more opaque molegro virtual docker user manual 4 Preparation Molecules can be imported into MVD using the Import Molecule menu option located in the File menu A shortcut is provided from the tool bar by clicking on the File folder icon or using the Ctrl O keyboard shortcut Molecules can also be imported by dragging and dropping the molecular file into the main application window Currently MVD supports the fol
130. ec R lt 4 5 A and EElec R gt 4 5 A The second table Hydrogen Bonds and Strong Electrostatic Interactions shows a list of all hydrogen bond and strong electrostatic interactions between the ligand and the target atoms From the Options drop down menu it is possible to show or hide the table but it is also possible to toggle the table to display covalent bonds instead Show Covalent Bond Energies Finally the Options menu also makes it possible to toggle whether hydrogen bonds and strong electrostatic interactions should be visualized in the GUI Hydrogen bonds are visualized as dashed lines where strong hydrogen bonds appear more solid and strong electrostatic interactions are visualized as partial spheres oriented in the direction of the interaction Green partial spheres correspond to favorable interactions while yellow spheres correspond to non favorable interactions The bottom panel Summary atom energies displays the sum of all atom interactions Notice that this is not the full energy of the ligand Some interactions like covalent bonding energies and constraint energies are not included For a complete list of energy contributions see the Total Energy tab The Target tab displays a list of all targets atoms residues and molecules involved in an interaction with the inspected ligand or pose It is possible to switch between two views a Show Residue Molecule Contributions which shows protein residues and
131. ed in the GUI REBUILD The addlabel command works in the following way it scans the input string for known variables like ID HYB ELE see below and replaces them with their value That is the command label bond bond_number id will add a label of type bond number x to every bond underscores are replaced with spaces To clear all labels use label without any argument Variable Description Atom labels Syntax Addlabel string ID Internal atom index Hydrogen bond type non polar acceptor donor both The Dre HBOND variable below is probably of more use PC Partial Charge molegro virtual docker user manual 27 Appendix X Console and Macro Commands page 224 251 PC PC ignores atoms with no partial charge HYB Hybridization HYB HYB only displays hybridization for atoms with other i hybridizations than SP3 or unknown SP2 Labels SP2 hybridized atoms SYM Element symbol H C N ELE Element number IH Number of implicit hydrogens HBOND Hydrogen bond type shown as D A D A non polar HBOND HBOND ignores non polar atoms Shows the total energy of the atom ETOT This requires that the energy has been evaluated using the eval command PDB Atom Name Show PDB Atom Name PDB Index Show PDB atom index Bond labels Syntax Addlabel bond string ID Internal bond index Type Bond order single double triple aromat
132. eeeeeesseeesseeeees 104 6 5 GPU SCreeNIN G ratssewacsipecoudeapdeheentavanescaradwsnaracessbiawenapeniempansamenens 106 7 Analyzing the Docking Results sssssssssssrrrnssrrrrensnnnnrrrrnnnrrnnnnrrrnsenna 110 7 4 POSE Org niZef eenias ensinar KA A ANAR 110 7 2 Saving Molecules and Solutions Found s sssssssssssssssrrssssrrrsssrrrresns 117 7 3 Ligand Energy Inspect erriren aAA RA EEA AA RS 118 7 4 Ligand Map 2D DepictionS ssssssssssssssrrssssrrrnrsrrnrrnsnnrnrrnnnnnrresn 127 7 9 POSS Modifie ezres o o a a e AE EE 129 7 6 RMSD Mati Xisceuviseceetissdeusdsecon aaa a ara Ea A a aE 130 8 Sidechain Flexibility sssssssssuesssrrnsnsnrnrrrrssrrrrnssssrrrnssnrnnrrrnnrrrrrnnnrrrenns 131 8 1 The Setup Sidechain Flexibility Dialog ssssssssssssssrrrsssrrrrrrnrrrrrrsss 132 8 2 Sidechain Flexibility in the Docking Wizard ssssssssssssrsssrrssressrrnn 136 8 3 Sidechain Flexibility and Scripting sssssssssssrrsssrrrssssrrrrrsrrrrersenn 137 9 Displaceable WaAUCr iivissccwwsiasoeussecou save anini KAKARA 139 9 1 Docking with Displaceable Water Molecules cccccceeeeeeeeeeeeeeanes 141 9 2 Inspecting RESUS riere aaa AA a Ea ERa 143 10 Template DOCKING cuicctascdocesiedeient toes oio nibe e i E nea EBEE 148 10 1 Template Scoring Function s ssssssssssresrrissrrrsrrnrrrnnnisnrnnsrrrsrrrnna 148 10 2 Setting Up Template Docking ssssssssssssrrrrssrnnnrrsnrnrrrrnsnnrreresnrae 150 10 3 Docking with Templates tensii
133. en running the Preparation dialog However the assignment of charges is based on standard templates and charge assignments can be missing in some cases It is possible to manually assign partial charges to atoms by right clicking on the atom in question and selecting the Set Partial Charge menu option Bond orders can be manually assigned by right clicking on the bond in question and selecting the Set Bond Order menu option Notice that bonds are not visible in some visualization styles The most suitable view is the ball and stick style which can be set from the Rendering menu in the menu bar Flexible torsions in the ligand can manually be set rigid or flexible by right clicking on a bond and selecting the Set Flexibility menu option When automatically detecting and assigning flexible torsion angles using the automatic preparation procedure a root atom is chosen The root atom is used as root in the torsion tree which is used to construct the ligand conformation during the docking process Sometimes the docking performance can be improved by choosing another atom to be the root atom To manually set the root atom right click on an atom and select the Set as Root Atom menu option Notice that bonds are not visible in some visualization styles The most suitable view is the ball and stick style which can be set from the Rendering menu in the menu bar molegro virtual docker user manual 4 Preparation page 73 251 The Prote
134. ened and whether the sidechain should be allowed to be flexible during the docking or not Several options exist for choosing the relevant residues Add Closest to Active Ligand This will choose all sidechains which are close enough to the active ligand to interact with it More precisely for each given sidechain a sphere bounding all possible configurations of the sidechain is molegro virtual docker user manual 8 Sidechain Flexibility page 133 251 calculated and it is tested whether any atom in the active ligand is close enough to make a steric contact with an atom in this bounding sphere for the MolDock potential all steric contacts are cut off at a distance of 6 0 A Notice that the Active Ligand can be set in the Workspace Explorer window it is the ligand which name is prepended with an Active label Add Visible This will add all sidechains which are currently visible in the 3D Visualization window This feature can be used together with the Hide Residues dialog where it is possible to hide sidechains depending on the distance from some given object Add Selected This feature makes it possible to select sidechains directly in the 3D Visualization window A sidechain is considered to be selected if one or more atoms inside it are chosen Clear List Removes all sidechains from the list Remove Selected Removes all sidechains that are currently highlighted in the sidechain list Remove Non selec
135. ensive than the scoring function used during the docking simulation but it is generally better than the docking score function at determining the best pose among several poses originating from the same ligand The default reranking coefficients are listed in the file Misc Data RerankingCoefficients txt Predicting the experimental binding affinity of a protein ligand complex based on a static conformation of the ligand is a difficult task For instance energetic contributions from solvent interactions and entropy contributions are difficult to handle in the simplified models used in molecular docking While the rerank score in MVD provides an estimate of the strength of the interaction it is not calibrated in chemical units and it does not take complex contributions such as entropy into account Even though the rerank score might be successful in ranking different poses of the same ligand it might be less successful in ranking poses of different ligands It is possible to create more sophisticated measures for the binding affinity using Molegro Data Modeller New models can use the descriptors created by MVD during the docking run the descriptors are stored in the mvdresults file These descriptors include both terms extracted from the MolDock score function like the protein ligand hydrogen bonding energy and static descriptors not using the 3D conformation of the pose like the molecular weight or the number of nitrogen atoms Mo
136. er is ignored all file formats If one of the other alternatives should be used change the order of occurrence in the file before import a CONNECT records PDB format a SUBSTRUCTURE records are ignored during import but created when structures are exported Mol2 format Notice Although extensive testing and validation of the import and export of these file formats have been conducted parsing errors may occur Compliance with the file format standards protocols will reduce parsing problems significantly The import export routines used have been extended to handle deviations from the file format protocols but parsing errors may still occur Found parsing errors can be reported contact Technical Support or send email to support clcbio com Additionally Molegro Virtual Docker uses its own MVDML file format MVDML is a shorthand notation for Molegro Virtual Docker Markup Language and is an molegro virtual docker user manual 23 Appendix VI Supported File Formats page 214 251 XML based file format In general MVDML can be used to store the following information a Molecular structures atom coordinates atom types partial charges bond orders hybridization states a Constraints location type and constraint parameters m Search space center and radius a State information workspace properties a Cavities location cavity grid points Camera settings position and angle a Visualization settin
137. er of poses returned to a maximum of five Continue to the next tab The Errors and Warnings tab in the Docking Wizard shows potential problems with the docking setup if any It should not show any warnings at this stage Press the Next button to proceed to the last tab In the Setup Docking Execution tab see Figure 10 several choices are available for executing the docking simulation We will use the default settings the settings are further explained in Section 6 3 Finally the Output directory specifies where the docking data log file and found poses will be stored Choose a directory pressing the button or keep the default settings Setup Docking Execution Choose how to execute the docking Run docking in separate process Creates a script and executes i in an extemal process Run docking in multiple processes For docking muttiple compounds using muttiple CPU cores and GPU s CPU Processes 1 GPU s 0 5 Create a docking scriptiob but do not run it now Can be used to prepare larger docking runs e g on several machines Start job on Virtual Grid Virtual Grid docking is only enabled when docking from a data source Edit script manually Data output Output directory C Users Molegro Documents MVD Data DockingOutpt ammm Save found poses as MVDML MVD XML format Pose name pattem SID SNAME e g 01 molecule mvdml V Create SMILES in MVDResutts file The generated script the logfile and the f
138. evaluates the affected part of the molecule and chooses the value which results in the lowest energy contribution The torsion angles are chosen from one of three distributions depending on the hybridization of the atoms the bond connects either sp2 sp2 sp2 sp3 or sp3 sp3 If the generated pose has an energy below energy threshold it is accepted into the initial population for the simplex evolution algorithm molegro virtual docker user manual 29 Appendix XII MolDock SE page 244 251 The simplex evolution algorithm performs a combined local global search on the poses generated by the pose generator The local search is performed using the Nelder Mead local search algorithm but unlike Nelder Mead s original scheme the algorithm has been extended to take the position of the other individuals in the population into account At each iteration a random individual is chosen The representation of this individual determines the first point of the simplex in the N dimensional search space Then N additional individuals are chosen and their representations define the remaining N points of the simplex a simplex in N dimensions has N 1 points Notice that Neighbour distance factor parameter determines how much the initial simplex should be enlarged or shrinked see below In order to use the search algorithm choose Search algorithm gt Algorithm gt MolDock SE from the Docking Wizard The following parameters can be set
139. f the different programming model for the GPU there are certain limitations when doing GPU Screening The following features can not be used when docking with GPU Screening a Constraints are ignored during docking both hard and soft constraints but notice constraints are taken into account when re evaluating using the CPU scoring function a Sidechain flexibility can not be enabled a Displacable water is ignored No support for Molegro Virtual Grid but notice that it is possible to use GPU Screening together with KNIME molegro virtual docker user manual Analyzing the Docking Results The Pose Organizer is used to inspect poses found see Figure 76 It allows you to browse the list of current poses to see detailed information about specific energy contributions to visualize hydrogen bonds electrostatic interactions and to calculate ranking scores and estimate binding affinity energies The Pose Organizer can be invoked in several ways It is automatically displayed after a docking result file with mvdresults file extension has been imported to MVD by dragging and dropping the file into MVD using File Import Docking Results mvdresults or by dragging and dropping the DockingResults icon pmi located in the lower left corner of the Molegro Virtual Docker Batchjob dialog onto the MVD application Otherwise it can be invoked by using the context menu on the Poses category in the Workspace Explorer
140. final tab see Figure 71 three choices are available for executing the docking simulation Run docking in separate process is the default choice which creates a MVD script that is executed in an external process Chapter 17 describes the MVD Scripting Interface in more details A copy of the current workspace is used so the user can continue working with the current workspace without interfering with the docking simulation e g add remove molecules change preparation etc The second choice Create a docking script job but do not run it now creates a docking script using the currently selected parameter settings The generated script is saved in the directory specified in the Output directory see below and can be used to start up the docking simulation on other computers The third choice Run docking in multiple processes makes it possible to use multiple cores or GPUs during the docking simulation see Chapter 6 4 for more information on docking with multiple processes The fourth choice Start job on Virtual Grid creates a molegro virtual docker user manual 6 Docking Functionality page 101 251 grid job and spawns the Virtual Grid Controller see Chapter 15 for more details about Virtual Grid execution When enabling the Edit script manually option a tab page containing the MVD script is shown making it possible to manually edit the script before starting the docking run The Output directory specifies where the docking data
141. for the PLANTS scoring function It is also possible to toggle on Displaceable water evaluation and set the corresponding entropy reward if that option was used during docking See Chapter 9 for more details about the displaceable water model used in MVD and the additional information available in the Ligand Energy Inspector 2 Ligand Energy Inspector Ligand pose XK2_263 Hide other ligands Ligand Targets Total Energy Settings Scoring function PLANTS Scoe V Include hydrogens in torsion tem Use original Plants setup Displaceable water evaluation Displaceable water Entropy reward for each water displaced 0 00 Copy tables to clipboard Figure 83 Settings tab page for PLANTS Score 7 4 Ligand Map 2D Depictions The Ligand Map makes it possible to depict molecules ligands and poses in the workspace in 2D This makes it easier to inspect the molecules make selections and to analyze receptor interactions The Ligand Map can be toggled on and off using the Ligand Map button on the tool bar in the main molegro virtual docker user manual 7 Analyzing the Docking Results page 128 251 window 8 thvrmvdml Molegro Virtual Docker File Edit View Rendering Preparation Docking Tools Window Help DEBE ADD O oo ao eae uae tems Options Workspace Unnamed 3 O Cavities 1 O Constraints 1 XK2_263 A Hide other ligands poses p jands 1 g Pro
142. gands Selected cells 299 Figure 109 User Interface of Molegro Data Modeller Molegro Data Modeller comes with its own separate manual The manual may be accessed using the application menu in either Molegro Virtual Docker or Molegro Data Modeller using Help Molegro Data Modeller Manual The manual is also available in the Help folder in the installation directory Molegro Data Modeller is not restricted to working with Molegro Virtual Docker and can be used with many kinds of data For instance Molegro Data Modeller may be used to build QSAR models for compounds without a 3D structure It is possible to run Molegro Data Modeller as a stand alone application by invoking the executable mdm exe or mdm directly from the installation directory or using the desktop or start menu shortcuts only available on Windows molegro virtual docker user manual 14 Molecular Descriptor Calculations The Descriptor Calculation Wizard offers an interface for calculating molecular descriptors for small molecules Molecular descriptors are sets of numbers which quantifies and characterizes certain characteristics of a molecule Several classes of molecular descriptors exists For instance molecular weight is a molecular descriptor which only depends on the molecular formula for a given molecule but descriptors may also rely on connectivity information 2D or topological descriptors or may rely on the actual 3D
143. generate and save a generated script Clears the current workspace All molecules are removed from the workspace molegro virtual docker user manual 28 Appendix XI Script Commands page 236 251 PARSERSETTTINGS lt initstring gt Determines the settings for the molecular parsers used to import the molecules The settings string is composed of semi colon separated pairs of a parameter key and its corresponding value The different parameters are breakUnrealisticBonds if enabled this option will break ignore unrealistic bonds parsed from the molecular file for SDF and Mol2 files only Default value is false combineMoleculeFragments if enabled this option will combine molecular fragments Mol2 substructures or small PDB molecules with same chain ID instead of importing them as independent molecules Default value is true useSybylForHybridization if enabled Sybyl atom types will be used to determine hybridization if they are available during import Otherwise the default geometric heuristic is used see Appendix VII Automatic Preparation for details moleculeNameField if a text string is specified e g moleculeNameField id SDF molecules containing a data header with the given name will use the content of this header when naming the molecule instead of using the first line in the SDF header The first header line will also be used if the file does not contain the specified data header
144. gs e g style and color of molecules rendering options hydrogen bonds and electrostatic interactions See description of Visualization Settings dialog for an overview of all settings Notice Purely graphical objects e g labels interactions annotations backbones and surfaces are not saved molegro virtual docker user manual 24 Appendix VII Automatic Preparation The principles behind automatic preparation in MVD are described below omaticity a All rings closed loops are identified a These rings are weeded out until a smallest subset capable of covering all ring bonds remains m These rings are considered aromatic if 1 For 5 cycles the mean torsion angle is less then 9 5 2 For 6 cycles the mean torsion angle is less then 12 a If the aromatic ring contains an atom which has out of plane bonds it is degraded to be non aromatic Notice that this is only a geometrical check for aromacity It does not include more advanced checks such as Huckel s rule and may fail on overlapping ring systems a All atoms with average bond angles gt 155 are marked as SP1 a All atoms with average bond angles gt 115 are marked as SP2 a All remaining atoms are marked SP3 a All atoms part of aromatic rings are marked as SP2 Ensure that if an atom is SP2 or SP it must be connected to another SP or SP2 or a terminal atom Otherwise the atom is degraded i e SP2 gt SP3 molegro virtual d
145. gs the size of the active search space is used For other values the crop distance is defined from the center of the current reference ligand Crop distance is measured in Angstrom If crop distance is negative all atoms in the protein will be taken into account Notice that the docking duration increases with the number of atoms It is advised to keep the default settings of 0 tabuclustering enabled rmsd threshold score penalty rmsd evalution mode e Enabled turns Tabu clustering on or off The possible values are true false e rmsd threshold determines how close two poses must be before being punished It is measured in Angstrom with a default value of 2 0 e The score penalty decides the amount that will added to the score function to punish poses which are close in terms of RMSD The value should be positive and has a default value of 100 e The rmsd evaluation mode is either id or automorphisms depending on whether the RMSD should be calculated using matching ids the fastest or by taking all automorphisms of the ligand into account more accurate but slower The default is id When tabu clustering is enabled in the Docking Wizard with default settings it creates the following initialization fragment tabuclustering true 2 100 id DisplaceWater true false Determines whether displaceable water evaluation should be included or not DisplaceWaterReward 0 0 10 0 The entropy reward for displaci
146. gy 18 3727 RMSD 6 59653 13 24 14 117 Iteration 30 Lowest Energy 2 66371 RMSD 6 88937 13 24 14 576 Iteration 40 Lowest Energy 61 0253 RMSD 7 68848 Results TH ents mvo Data DockingOutput 228 DockingResults mvdresults Status Finished Figure 11 Docking Progress dialog While the simulation is running the energy of the currently best found pose the pose with the lowest energy can be observed on the Graph tab page see Figure 12 The graph shows the docking score in arbitrary units as a function of number of iterations performed by the docking search algorithm molegro virtual docker user manual 2 Docking Tutorial page 20 251 Batchjob started ma 27 aug 10 12 41 2012 Elapsed 00 00 16 Finish estimated 10 13 21 Remaining 00 00 23 Working path C Users Mikael Documents MVD Data DockingOutput 227 Curent ligand 5 10 runs me Log Poses current ligand 13 Poses al Blue Energy of best pose Red Mean Energy of candidate population Status Docking BEN_1 AJ from Unnamed _complex mvdmi Figure 12 Docking search progress Let the simulation run for a while 1 2 minutes or so The docking engine should find a good solution within 800 iterations The simulation will eventually time out on its own after 2 000 iterations or about 100 000 evaluations or if the simulation has converged Notice Becau
147. gy MAD Sisse i aa T Aa a EE E ai 64 A Pre Dall Atl ureesenorinininn a e a a a a EEEE RE 67 molegro virtual docker user manual page 4 251 4 1 Import of MOM GUNS Seance cececceuicececsestiaedeebisedensascencteccsansacecaretveneseicenn 67 4 2 AUTOMALIC PREDSl AON vitsccecerserccpertissesstuasviseiieend RAAR TENANE EEEE nares 68 4 3 Mahal Prepal ation scccdssinetigd ive ens rorci tenesi Deo i a e O ETE RE E 71 4 4 Protein PreparauOninccicctcciieiiaetepenauiwcntaniheieietameueniokenteniniasantees 73 4 5 The Protonation Tad vicsceckistenekseieeeiseneeveedad eunnds EAN EEKAN 73 4 6 The Mutate and Optimize Tab cccccesceeeeeseceeeeseseensseeeensseeeenaaees 76 4 7 We Settings TalsisccecconsosncteSusncxanasrexsareedns aisenacarseseasweaneavectseasuetaeen 77 4 8 Customizing the Protonation TemplateS sssssssssesrrssrrrsrrrsrrrsrrnns 78 5 Data SOUS wxiscsixvicnicunianseguinndcaviaeivensielegniaedeieiaeierninyiesiieeexnivelexemnls 81 5 1 Data SOURCES SYNUEX wiinaiersinaisiicigeetiviiivicinsierusseridereeer ie 82 5 2 USING Datla SOUNCES cemssarcinsiescrai ne ciediaenisdandeuainiatasirieusst inte NE 83 6 Docking Functionality seisseen annant aana EREA E EEEREN 86 6 1 Ca vity Predicti Mis cmoo i EE SEEE E CEEE D KEA EREE 86 6 2 CONS AINS sissi naaa AANKAN KANA EAA VAA NN 87 6 3 Docking Wizard sssssssssssrssssrrrsrsrnnrrrrnnnrrrrnnnrrresnnnrrrrennnnerennnnnne 91 6 4 Run Docking in Multiple ProceSses ccceseceeeseeeeees
148. h the ligands selected for docking Notice If more than 10 ligands are present in the workspace a subset of the ligands can be selected for docking using the Specify ligand range option not shown on Figure 64 It is also possible to dock ligands from an external data source see Section 5 2 for details about data sources The last option From KNIME workflow makes it possible to dock ligands using the KNIME workflow system See the Molegro KNIME Extensions Installation amp usage guide for more details available from www molegro com knime MVD includes Mo Dock Score THOMSEN 2006 and PLANTS Score KORB 2009 for evaluating docking solutions The Mo Dock Score is further described in Appendix I MolDock Scoring Function and PLANTS Score is described in Appendix II PLANTS Scoring Function Grid based versions of the scoring functions are also available The Mo Dock Score Grid is a grid approximation using the same energy terms as the MolDock Score except that hydrogen bond directionality is not taken into account PLANTS Score Grid is a grid approximation using the same energy terms as the PLANTS Score The grid based scoring functions provide a 4 5 times speed up by precalculating potential energy values on an evenly spaced cubic grid see Appendix XIV Grid based Scores for more details The following options are available for the MolDock Scoring functions The Ignore distant atoms option is used to ignore atoms far away from
149. hain The degrees of freedom that are minimized during the docking simulation are the torsional angles in the sidechain Max T The temperature factor or B factor is a measure of how much a given atom vibrates around its position in the crystallographic model This can be useful since a high B factor may indicate that the residue is likely to be flexible Max T is the single highest temperature factor of all heavy atoms in the sidechain Columns in the list can be toggled on or off using the context menu on the sidechain list view Choose molecules to take into account a Proteins 2 2 a Ligands 5 5 The Advanced tab allows you to determine which structures in the workspace should interact with the sidechains during the minimization By default all molegro virtual docker user manual 3 User Interface page 48 251 structures ligands cofactors water are taken into account when minimizing If you work simultaneously with multiple conformations of the same receptor in the workspace make sure that only the specific conformation to be minimized is selected as an interacting structure The Choose Visible button selects all structures which are currently visible in the workspace as interacting structures The lower panel Minimization settings handles the setup of the minimizations algorithm The minimization algorithm is Nelder Mead simplex minimization first running a specified number of
150. he Docking Wizard The scoring function combo box allows to choose between the docking scoring functions available in MVD MolDock Score and PLANTS Score For MolDock Score the following options are available Internal ES toggles whether internal electrostatic interactions should be calculated for a pose Internal Hbond no directionality toggles whether a pose should be allowed to have internal hydrogen bonds notice that hydrogen bond directionality is not taken into account for internal hydrogen bonds in ligands and Sp2 Sp2 Torsions determines whether an additional dihedral term should be added for taking Sp2 Sp2 bonds into account see Appendix I MolDock Scoring Function It is also possible to toggle on Displaceable water evaluation and set the corresponding entropy reward if that option was used during docking See Chapter 9 for more details about the displaceable water model used in MVD and the additional information available in the Ligand Energy Inspector molegro virtual docker user manual 7 Analyzing the Docking Results page 126 251 et Ligand Energy Inspector Ligand pose XK2_263 Hide other ligands poses Ligand Targets Total Energy Scoring function MolDock Score Ligand evaluation Intemal ES E Intemal HBond no directionality Sp2 Sp2 torsions Displaceable water evaluation E Displaceable water Entropy reward for each water displaced 0 00 Hydrogen bond evaluation
151. he chosen proximity distance Poses work the same way molegro virtual docker user manual 3 User Interface page 34 251 For cavities the distance to each single cavity point is considered when hiding objects The residues and molecules are dynamically shown hidden when the Proximity slider is moved The lower pane of the Hide Residues dialog allows you to restrict the types of residues shown by toggling the appropriate button If a given residue type is not within proximity distance as defined in the panel above the button corresponding to the type will be grayed and can not be toggled si Select Which Residues to Hide IY Only show residues close to CSO_67 A E Proximity p E Hide distant molecules water ligands Figure 24 Hide Residues dialog The Show backbone only check box can be used to toggle whether side chains are visible or not Cropping It is possible to delete molecules from the workspace in order to remove non relevant regions To crop molecules invoke the Hide Residues dialog and adjust the settings until the desired residues and molecules are displayed before clicking the Crop Molecules button A dialog will show which structures will be kept the checked molecules and which will be discarded Notice that proteins are split and cropped on a per residue basis hidden residues will be discarded and visible residues will be kept All other molecule types are kept or discarded
152. he docking scoring function used is below a given tolerance When all individuals have been refined the best found individual named iteration best solution will be further refined using the same Simplex algorithm again but with a lower tolerance Tolerance iteration best solution When max iterations have occurred the algorithm terminates and returns the best found solution s By enabling the Constrain poses to cavity option in the Docking Wizard the Iterated Simplex algorithm uses a cavity prediction algorithm introduced in Appendix IV Cavity Prediction to constrain predicted conformations poses during the search process More specifically if a candidate solution is positioned outside the cavity it is translated so that a randomly chosen ligand atom will be located within the region spanned by the cavity Naturally this strategy is only applied if a cavity has been found If no cavities are reported the search procedure does not constrain the candidate solutions The Iterated Simplex algorithm is generally more robust w r t reproducing docking results with similar scores than the MolDock SE and MolDock Optimizer Therefore the default number of runs in the Docking Wizard is set to 1 In some cases more runs e g 5 might be necessary to identify good binding modes in particular when docking very flexible ligands molegro virtual docker user manual 30 Appendix XIII Iterated Simplex page 247 251 In order to use the
153. hoice and the default choice or if intrinsic ligand symmetries should be taken into account which is slower but more accurate Tabu clustering is performed per ligand when a new ligand is docked the tabu list is cleared Notice that the tabu list gets longer for each run so when docking many runs for each ligand tabu clustering may slow the system For virtual screening runs the Virtual screening mode option is particularly suitable for returning a percentage of the top ranked compounds found during the virtual screening run the percentage can be specified in the dialog Since the set of top ranked poses found are updated dynamically during the virtual screening run more than the specified percentage of poses will be returned Notice setting the percentage to 0 will toggle off pose clustering and the best scoring pose for all ligands will be returned The Docking Wizard reports errors and warnings found such as non bonding atoms in molecules steric clashes between atoms unsupported residues missing hydrogens in proteins etc A detailed description of each warning and error is shown at the bottom of the Errors and Warnings tab see Figure 70 molegro virtual docker user manual 6 Docking Functionality page 100 251 Errors and Wamings Waminags Category Workspace contains no cavities Detailed description Cancel Figure 70 Any warnings or errors are shown on the last page in the wizard In the
154. ial is then evaluated for all these distances but only the lowest energy is returned as the soft constraint energy That is only the atom with the lowest energy relative to the constraint potential is taken into account The reason for this is that if you for example want to reward ligands with a hydrogen acceptor close to hydrogen donor in the protein it does not make sense to punish other atoms in the vicinity of the constraint if one hydrogen acceptor is already at its optimal distance from the donor Another type of constraint is the Ligand Atom Constraint It is used to constrain a specific ligand Since Ligand Atom Constraints are defined using a list of atom IDs they are specific to ligands and are only applied to the ligand on which they are defined To create a Ligand Atom Constraint select a number of atoms in the same ligand in the Visualization Window Ensure that no other objects are molegro virtual docker user manual 6 Docking Functionality page 90 251 selected and choose Constraint Selected Ligand Atoms from the context menu right click mouse button It is also possible to use the context menu on a single ligand atom Create Ligand Atom Constraint without performing a selection The Ligand Atom Constraint dialog will appear see Figure 63 It is possible to modify the list of atoms in the ligand by entering a comma separated list of IDs Notice Ligand Atom Constraints are always soft constraints It is poss
155. ial may slightly differ on Linux and Mac OS X versions Molegro Virtual Docker contains a built in version checker making it easy to check for new program updates including new features and bug fixes To check for new updates select Help Check for Updates A window showing available updates and details about changes made will appear see Figure 1 molegro virtual docker user manual 1 Introduction to Molegro Virtual Docker page 10 251 Latest version available Your current version 2009 3 2 1 Changes June 9th 2010 MVD Version 4 1 0 Molegro Virtual Docker 4 1 0 updates the Data Analyzer and improves Molegro Virtual Grd performance and stability Notice that it is possible and recommended to update trial licenses as long as the trial license key is still valid February 10th 2010 MVD Version 4 0 2 Molegro Virtual Docker 4 0 2 is a minor update which adds better support for very large molecules foreign unicode characters in MVG scripts and fixes a few bugs Anew version has been found Please go to www_molegro com to update your application Figure 1 Check for updates molegro virtual docker user manual 2 Docking Tutorial This tutorial will go through a simple docking exercise by redocking a co crystallized ligand to its native binding site The tutorial will highlight aspects such as import and preparation of molecules conducting the actual docking run and visual inspection of the poses fo
156. ible to choose whether the chosen atoms in the ligand should be rewarded or penalized for contacts with the target molecules proteins cofactors and water igand Atom Con This Ligand Constraint is bound to ligand 0 Constrain the following atoms in ligand comma separated list of ID s 6 Ligand constraints are specific to one ligand Soft constraint Penalize chosen atoms for making contacts Energy penalty 500 gt Reward atoms for making contacts Energy reward 500 Define atom contact threshold A 4 00 Figure 63 Ligand Atom Constraint dialog The criteria for contact used here is purely based on the distance between the chosen ligand atoms and the closest atom in any target molecule The distance threshold for defining contacts can also be customized using the Define atom contact threshold A input field Typical Uses Constraints are useful if something about the system is known in advance If perhaps a hydrogen bond from a hydrogen donor was known to be present a distance constraint could be set up at the position of the protein hydrogen donor and a hard constraint could force hydrogen acceptors in the ligand to satisfy the hydrogen bond molegro virtual docker user manual 6 Docking Functionality page 91 251 6 3 Docking Wizard When all the molecules have been prepared the docking can commence To start the Docking Wizard select Docking Docking Wizard A shortcut is provided by clicking
157. ic Shows the total energy of the bond ETOT This requires that the energy has been evaluated using the eval command Residue Labels Syntax Addlabel residue string ID Internal residue index LONGNAME Full residue name histidine cysteine NAME 3 letter abbreviation HIS CYS LETTER 1 letter abbreviation molegro virtual docker user manual 28 Appendix XI Script Commands This appendix describes all the script commands that are available in MVD Some script commands require a molecule target these can be described using the following syntax Ligand O the ligand with ID 0 Ligand 4 5 6 the Ligands with IDs 4 5 and 6 Multiple IDs are separated by comma Ligand 50 60 the Ligands with IDs from 50 to 60 both included Ligand ranges are specified by a Ligands All ligands By using the plural form of a category all molecules in it are selected The categories are Pose Cofactor Protein Water Ligand Poses Cofactors Proteins Ligands Waters All Poses Cofactors Proteins Ligands and all Water molecules Multiple targets can be concatenated using a semi colon All imports all structures Notice The IDs of molecules are defined by their order of occurrence in the workspace All indices are zero based meaning that the first ligand will have index 0 the second index 1 and so forth molegro virtual docker user manual 28 Ap
158. ical Feature Distance Matrix DescriptorS s ssssssssrrrerresrresrss 175 ES Molaro Virtual GiiC coccontesceunsicasdussaneseadanedioessecduaessacusquseenneseeeemeneeds 179 15 1 Sec rit Consideration Serseri eied ig ee a E EEA 180 15 2 Network and Firewall ISSUCS cccceeseeeeeeeeeeeeseeeeeeseeseenneenees 180 15 3 LICENSING iccsentin teins a a Na Ea E A ane 181 15 4 Running the AGSIES ocscccccsencunzieintecececamseneumetccsede est warugeentadcuaia bic 181 15 5 Nine Agent GU ccociressovess sc deanesonandcoreuasesneuoctaanssdnasesscpenaasagersoges 182 15 6 ONS Moderen roge sereo ea tne E EEEa EEEE a 183 15 7 Agent Web Interface ss ccscowtesicnivscdenvsiwsweseessseesniasex EAA ARa 185 15 8 The Virtual Grid Controller uc sve iascsenwas teviwd do deeedesiveaeveraieeeet eG sacs 185 15 9 Combining ReSUNS ccccccwrtcnscwehd anders emendclencesdsaueeecssresenigouesspeaceaes 187 15 10 License ManagQementiciessincceccevacsnavecenmenriasiencseamweaser eaeemnnrareene 188 15 11 How Virtual Grid WGP ces vewicdstteaieds boetedabueteusbuntess debian de beeiaenesee 188 16 El Paincsccniscaanerscaiarieanesaicnieng E ARAA EAA A a 191 tS PDF Helper iisen en E E E ENA 191 16 2 TID Of the Day acere eiaa a E E E EA 191 16 3 The Molegro Website ssssssrsessssrrsssnsrrsnsnnnnsnnnnnnossnnnrronsannrrrnennn 192 16 4 Technical SUP PON Cine ccs tories detec e E N EEEE eee 192 17 Script INVGMACE iss couscusionsdeciixscanivxeduvbusdsuvgsagauelerseavlzan bedine
159. ifferent subsets of the molecules In this case it is necessary to run the Biomolecule Generator multiple times Also notice that biomolecules can be very large Always render the protein in wireframe before attempting to generate large biomolecules molegro virtual docker user manual 3 User Interface page 60 251 3 25 Structural Alignment of Proteins It is possible to structurally align proteins in Molegro Virtual Docker A structural alignment is done by matching a number of residues in two proteins and calculating the translation and rotation that minimizes the RMSD between the alpha carbons in the matched residues The Structural Protein Alignment dialog can be invoked by selecting Tools Structural Protein Alignment from the main menu Structural Prote n Alignmen Reference protein 2ACR A Protein to be aligned 1AH3 A Using the alignment above align additional molecules C Proteins 0 2 C 2ACR A 5048 atoms C 1AH3 A 3050 atoms B Ligands 3 5 O CO NAP_316 A 74 atoms AYA_1 A 9 atoms NAP_318 A 55 atoms TOL_320 A 38 atoms Match by residue type and PDB index Match by residue type and position Target offset 0 Figure 48 The Structural Protein Alignment dialog box The first step is to choose a reference protein and a protein to be aligned the target protein The target protein is the protein which will be translated and re oriented
160. ify ligand range from 1 W to 761 B Import small molecules as Ligands K K R K K E K S K R KK KK E vr Replace or add to workspace Add to current workspace Figure 53 Import Molecules dialog When all relevant molecules have been imported the molecules can be automatically prepared see next section MVD automatically tries to identify cofactors a molecule is considered a cofactor if it has less than 5 heavy atoms or its name is included in a list of common cofactor names like HEM SO4 PO4 If this is not desired it is possible to override cofactor recognition by checking the Import cofactors as ligands option 4 2 Automatic Preparation Some molecular file formats support information about bond type and charge e g Mol2 while others do not e g PDB In order to maker proper predictions it is important that the structures have been properly prepared That is that the atom connectivity is known and that the correct bond order and charges have been assigned The Prepare Molecules dialog allows the user to perform the necessary molegro virtual docker user manual 4 Preparation page 69 251 preparation It is invoked automatically when importing Mol2 SDF or PDB files and can be invoked manually by selecting Preparation Prepare Molecules or by using the context menu e g Prepare Ligand on molecules in the Workspace Explorer Assign All Below Assign b
161. igand from collapsing Af fil omy a ot pile 10 4 Inspecting Results i After the Docking engine has finished aligning or docking the ligands the resulting poses are imported back into MVD in the same way as an ordinary docking result molegro virtual docker user manual 10 Template Docking Settings Dynamic update Show hydrogen bonds Orient hydrogens to optimal position Show electro Table columns static interactions Display only residues closer than A 6 00 Show matching receptor configuration Re evaluation of poses Ranking Score coefficients unk MVD Misc Data RerankingCoefficients bt i Recalculate Energies O Protein O Water O intemal O Torsions O Bectro O BectroLong M HBond O mw OD LEI oO LE DisplacedWater The interaction energy between the pose and the protein The interaction energy between the pose and the water molecules The intemal energy of the pose The number of chosen rotatable bonds in the pose O Soft Constraints The energy contributions from soft constraints Short range electrostatic proteindigand interations r lt 4 5 Long range electrostatic proteindigand interations r gt 4 5A Hydrogen bonding energy C Heavy Atoms Number of heavy atoms Molecular weight in dalton Ligand Efficiency 1 MolDock Score divided by Heavy Atoms count Ligand Efficiency 3 Rerank Score divided by Heavy Atoms count m Doc
162. ilable for detecting cavities see Figure 61 allowing to customize the sensibility and type of cavity search The Cavity Prediction dialog can be invoked via the context menu in the Workspace Explorer in molegro virtual docker user manual 6 Docking Functionality page 87 251 the Proteins category or by selecting the Detect Cavities menu option from the Preparation menu For large targets a global search for cavities may be slow or result in too many possible binding sites It is possible to restrict the search to the sphere defined by the current search space using the Restrict to search space checkbox This makes it possible to define an approximate location of the most likely interaction sites and then perform the cavity detection within this volume The advanced settings are described in Appendix IV Cavity Prediction Notice it is possible to choose which molecules should be taken into account when performing the cavity detection Cavities found are listed in the Workspace Explorer in the Cavities category Visualization of the cavities can be toggled on and off Moreover volume and area are listed for each cavity Cavities may be deleted from the workspace by selecting them in the workspace explorer and choosing Remove cavity from workspace It is also possible to merge cavities by choosing Merge With Other Cavity Notice If no cavities are identified ligands can only bind to the surface of the protein or the c
163. in Preparation dialog allows you to inspect the proteins in the workspace for structural errors Such as missing atoms or erroneous bonds and to inspect and change the protonation state for the residues It is also possible to mutate residues for instance replacing an asparagine residue with an aspartic acid residue and subsequently energy minimize them The protein preparation dialog can be invoked by choosing Preparation Protein Preparation from the main menu bar When the protein preparation dialog is invoked a list of residues is shown All residues with potential errors are initially highlighted on the list and emphasized in the 3D view with yellow or red spheres corresponding to the two different kinds of residue errors a Residues with structural errors These kinds of residues do not match the atom and bond information in the protonation templates explained below They might have missing atoms or invalid bonds between the atoms Notice that terminal residues does not always match the standard templates they may contain additional atoms such as a terminal oxygens OXT It is not possible to change protonation for residues with structural errors but they may be reconstructed by using the Mutate and Optimize tab to mutate to a residue of the same type These residues are shown with red spheres in the 3D view a Residues with a valid atomic structure but with an invalid protonation These kinds of errors occur if the residue
164. in their entirety 3 10 Workspace Finder The Workspace Finder located in the far right side of the MVD Toolbar see Figure 25 allows you to quickly search for molecule names and residue atom IDs in the workspace The Workspace Finder is invoked by typing characters molegro virtual docker user manual 3 User Interface page 35 251 in the search box text field A result is selected by pressing the Return key Pressing the Escape Esc key or mouse clicking outside the Workspace Finder window will cancel the current search query 1stp mvdml Molegro Virtual Docker File Edit View Rendering Preparation Docking Tools Window Help S amp S oe ai Q a oa ad Hydrogens Fog Hide Residues Items Workspace New F Backbones 1 O Cavities 1 O Constraints 1 Interactions 11 Ligands 1 Active BTN_300 Proteins 1 O Surfaces 1 O Water 84 Property Value Position 6 62521 1 8526 Residue Trp 108 Intemal residue 95 Atom ID 1550 Element H 1 PDB atom name H PDB atom ID Not Available Tripos atom type H VdW radius 12A Covalent radius 0 23 Hydrogen bondi Nonpolar Partial charge 0 Hybridization Temneratune 0 Figure 25 Workspace Finder dialog When a name or ID number or part of it is typed in the search box the Workspace Finder will present a list of matches a maximum of 30 matches is returned It is a
165. ion and then creates a small script file which contains instructions on how the docking should proceed The default behavior for the Docking Wizard is then to spawn a script interpreter in another process the script interpreter and the main application runs completely separated and execute the script However greater flexibility is possible by writing custom scripts for instance this makes it possible to dock a number of ligands against several distinct targets It is also possible to split large docking runs into several scripts and run them on different machines Notice A MVD script job basically runs in a single thread This means that as such MVD will not utilize multiple CPU s or dual core processors However by splitting the job into two or more jobs and running them concurrently all available CPU s can be utilized Text file scripts are ordinary text files saved with the mvdscript file extension In order to run a text file script simply start MVD with the text file script name as the argument molegro virtual docker user manual 17 Script Interface page 194 251 Example mvd docktest mvdscript This will spawn the Script Progress GUI with information on how the script parsing is progressing Molegro Virtual Docker Batchjob Finished G Batchjob started ti 28 aug 14 15 34 2012 Hapsed 00 00 00 Skip run Finish estimated Simpl Working path C Users Mikael Documents MVD Data DockingOutput 232
166. ions v Workspace New Ligands 1 Proteins 2 Property Value Position 10 435 15 837 Atom ID 27 E Element C 6 F PDB atom name C PDB atom ID Not Available Tripos atom type C ar Plants atom type Not Defined Hydrogens 1 VAMI radine 17 Time Description Figure 4 The imported structure In order to inspect the imported ligand hide the protein by clicking on the check box next to the Proteins category in the Workspace Explorer see Figure 5 molegro virtual docker user manual 2 Docking Tutorial page 15 251 Workspace Explorer tems E Workspace New Figure 5 Hiding the Protein Now zoom in on the ligand see Figure 6 Zooming can be performed using either m the scroll wheel on the mouse m by pressing and holding both mouse buttons a by pressing shift and holding left mouse button It is also possible to choose Fit to Screen from the context menu for ligands in the Workspace Explorer Notice that the ligand has been assigned bond orders aromatic rings have been detected and explicit hydrogens have been added Also notice that some bonds are green These bonds will be set flexible during the docking simulation If a bond should be held rigid during the simulation right click on it and choose Set Flexibility from the context menu Figure 6 Inspecting flexible bonds Next we will add a surface to get an impression of the structure of
167. is possible to run it as a console application as well This is done by specifying the command line option nogui The following command line options are available nogui Starts the agent without a graphical user interface This makes it possible to run the agent in the background on systems without a graphical user interface for instance running the agent on a remote Linux system using a shell Notice the web interface see Section 15 7 makes it easy to see the status and error log of the running agent mvdpath Specifies the path of the MVD executable Example virtualgrid mvdpath C program files Molegro MVD bin mvd exe The path is stored by the OS so it only necessary to set it once The path can also be set in the GUI molegro virtual docker user manual 15 Molegro Virtual Grid page 184 251 workingdir Specifies the directory the grid agent use for temporary files files received from the controller or docking result files Example virtualgrid workingdir C tempdir The path is stored by the OS so it only necessary to set it once The path can also be set in the GUI priority Specifies the process priority when launching MVD instances Notice that the process priority is normally set by the controller Specifying an agent priority overrides the controller settings In most cases is not necessary to set this value The process priority specifies how the OS schedu
168. is software is licensed to Mikael Molegro Trial 15 10 05 396 The license will expire on oktober 30 2013 15 10 05 396 Using working path C Users Mikael Documents MVD Data 15 10 05 663 Deleted temporary file C Users Mikael Documents MVD Data Temporary Files Template Terms 15 10 05 761 Checking for new MDM updates Latest version listed on web 2011 2 6 0 Figure 100 Using Molegro Data Modeller for inspecting the docking template By analyzing a set of ligands aligned using template docking it is possible to create a regression model of a experimentally known quantity This would allow for a 3D QSAR approach based on the values of the group center overlap molegro virtual docker user manual 10 Template Docking page 154 251 10 3 Docking with Templates Whenever a template definition is present in the workspace the following tab appears in the Docking Wizard after the first tab where the input ligands are chosen Template Docking Docking using Ligand Templates A Docking Template has been found in the workspace V Enable template scoring Overall strength 500 00 7 Use energy grids Resolution A 0 40 Figure 101 The Template Docking Tab in the Docking Wizard The Overall strength determines the normalization of the similarity score A ligand perfectly matching the template gets an energy contribution corresponding to the specified strength e g per default a perfectly matching ligand gets
169. ites existing filenames named lt filename pdb gt Examples DOWNLOAD 3ptb AS 3ptb pdb IMPORT All FROM 3ptb pdb DOCK 28 2 Flow Control MVD also provides a couple of simple commands for controlling the script flow If more complex execution control is needed consider using the Python wrapper to control to scripting engine Notice The variable system in the script parser is strictly string based which means that the script parser simply substitutes occurrences of variable names with the current value before parsing the string Also notice that this means that it is important to be careful when defining variable names and ensure that they do not overlap e g do not define two variables named PDB and PDBS since the script parser will substitute part of the variable name PDBS with the value of PDB molegro virtual docker user manual 28 Appendix XI Script Commands page 242 251 FOR lt VAR gt IN lt VALUELIST gt ENDFOR The FOR command can be used to iterate though a set of possible values The VALUELIST must be a comma separated list of values FOR commands can be nested it is possible to have a FOR command inside another FOR loop Variables must start with a identifier Example docking multiple complexes FOR SPDB IN 3PTB 1HVR 1LIC 1TMN SPDB will be replaced by the appropriate value in the loop LOAD C BENCHMARK S PDB mvdml RMSD ligand 0 DOCK NEW ENDFOR
170. izer allows you to inspect the poses and select which structures to keep by toggling the select box next to them At this point we will just add all found poses to the workspace First select all poses by manually checking them or use the Edit Check All menu Afterwards press the OK button molegro virtual docker user manual 2 Docking Tutorial page 22 251 2 3 Viewing the Results At this point it would be a good idea to save the workspace with the new poses added This can be done by selecting File Save Workspace This will save the workspace proteins ligands poses etc in MVD s own XML based format In order to export the poses to other formats the Pose Organizer can be used Revisiting the Pose Organizer First switch to the pose organizer view View Pose Organizer View Each pose is shown in different colors Next open the Pose Organizer select Docking Pose Organizer GG Pose Organizer 4 po Settings Name j MolDock Score Rerank Score RMSD HBond 00 XK2_ 232 142 181 165 0 524029 8 88757 1 eC ae 2O A lt A L 02 xk2_ 223 002 172 048 1 13816 9 6109 O 03 xk2_ 175 335 60 3827 3 03842 6 87344 Dynamic update notice disables multiple poses selection Only show top 1 poses for each ligand Open checked poses in Data Analyzer Sorting criteria Ist Ligand 2nd MolDock Score 3d None Pressing OK will keep 2 and ign
171. keepmaxposes int 5 excludeenergythreshold double 10000 clusterthreshold double 0 0 The following parameters are used by the MolDock Optimizer algorithm scalingfactor double 0 50 crossoverrate double 0 90 offspringstrategy int 1 earlytermination double 0 01 terminationscheme int 0 The following parameters are used by the MolDock SE algorithm creationenergythreshold double Default is 100 0 Poses are only added to the population if the value is this threshold Notice that when half of the iterations in the docking run have been used this threshold is automatically turned off in order to ensure that enough poses are created for the simplex evolution phase posegenerator int int int Set the Min Quick Max number of tries Default is 10 10 30 At each step at least min torsions translations rotations are tested and the one giving lowest energy is chosen If the energy is positive i e because of a clash or unfavorable electrostatic interaction then additional max positions will be tested If at one time it has not been possible to construct a component which do not clash the max tries number is molegro virtual docker user manual 28 Appendix XI Script Commands page 234 251 OPTIMIZER lt initstring gt lowered to the quick try value simplexsteps int default 300 The number of iterations of the Nelder Mead simplex minimization procedure performed at each step of the M
172. king Wizard and constrain candidate solutions to the region covered by the cavity by enabling the Constrain poses to cavity option in the Docking Wizard Notice It is important to select a search space Radius that allows the ligand to be positioned within the search space region typically between 15 and 20 A However the Radius should be set as small as possible to make the docking search efficient Likewise the Origin center of the search space region can be manually adjusted to focus the sampling of candidate solutions to a specific region This is particularly important if the cavity volume is much bigger than the ligand for large cavities focusing on one specific part of the cavity will significantly increase the docking accuracy m Search parameters The default settings for the docking search algorithm are generally applicable However in some cases e g for ligands with more than 15 torsions it can be advantageous to increase the Population size to 100 individuals or more a Multiple runs Because of the stochastic nature of the docking search algorithm it is recommended to make multiple runs for each ligand molegro virtual docker user manual 12 Obtaining the Best Docking Results page 167 251 protein setup Typically about 5 10 runs are needed to ensure convergence to the lowest energy solution For large ligands with more than 10 15 flexible bonds 20 50 runs are sometimes needed Additionally it is recommen
173. king Score Evaluated before post processing either Plants or MolDock EEE Similarity Score f docking templates are enabled The energy contributions from non displaced and displaced water interactions f enable _ Figure 103 Enabling the Similarity Score term page 156 251 It is important to notice that the Pose Organizer table only shows the contributions from the primary score function the Ligand Evaluator or the MolDock Score funtion The similiary contribution from the docking template is not shown per default In order to see the similiary score go to the Settings and enable Similarity Score from the list of table columns To see the score actually assigned to the pose during docking enable Docking Score this will be the sum of the similarity score and the chosen primary score function molegro virtual docker user manual 11 Customizing Molegro Virtual Docker Molegro Virtual Docker can be customized using the Preferences dialog which can be invoked from the Edit menu or by pressing F4 Preference settings are categorized in General Graphics Mouse and Parsing tabs In the General tab see Figure 104 the following settings are available a The Load most recent workspace on startup if any option toggles automatic import of the last used workspace a The Show tip of the day on startup option toggles whether the Tip of the day dialog box is shown during startup or not a The Check for
174. l 3 User Interface page 54 251 selector next to the light checkbox OpenGL Lights contain three different parts Ambient light always reaches an object independent of its position relative to the light source Diffuse lightning is dependent on whether the object faces the light source or faces away from it The reflected light is emitted equally in all directions Specular lightning is also dependent on the objects orientation towards the light source but the reflected light is emitted mainly in the direction of the reflected light ray creating highlights The Interactions tab Figure 43 on the Visualization Settings dialog allows you to customize the appearance of hydrogen bonds energy thresholds thickness of bond and color and electrostatic interactions energy thresholds and color shown in the Visualization Window lt Visualization Setting ie Hydrogen Bonds Minimum Maximum Eneray Thickness f 0 0 0 5 1 0 1 5 2 0 2 Electrostatic Interactions Minimum Maximum Eneray f B Negative Positive 5 0 3 0 1 0 10 30 50 Restore to Default Settinas Figure 43 Settings for hydrogen bonds and electrostatic interactions molegro virtual docker user manual 3 User Interface page 55 251 The Views tab Figure 44 in the Visualization Settings dialog controls the preset views the macros residing under the View menu item on the main window menu bar The upper panel on the tab a
175. l or a selection of the molecules available in the workspace see Figure 78 molegro virtual docker user manual 7 Analyzing the Docking Results page 118 251 i Cofactors 2 2 Proteins 2 2 1HVR A 920 atoms M TAVR B 920 atoms mma iLigands 1 1 E Notice Proteins and waters cannot be exported to MDL Mol files sdf sd mol mdl Output scheme One single file Figure 78 Export Molecules dialog Select which molecules to export To export molecules select File Export Molecules or Export Molecules from the Workspace context menu in the Workspace Explorer also available for proteins ligands cofactors and poses Notice Proteins and water molecules cannot be exported to SDF files To save the poses obtained from the docking runs either use the Export Molecules dialog described above or save the poses from the Pose Organizer dialog The Ligand Energy Inspector allows you to get detailed information about the energy interactions for a given ligand or pose The Ligand Energy Inspector can be invoked in different ways It can be started using the context menu in the Workspace Explorer by choosing Open Ligand Energy Inspector on any Ligand or Pose item It can also be started from the Pose Organizer using the context menu on any pose entry or by selecting Tools Ligand Energy Inspector Notice the ligand energy inspector evaluates the energy of the ligand or pose when invoked This mean
176. l cluster and the member is assigned to be the cluster representative 3 The remainder of the pool members are added to the most similar cluster available using the common RMSD measure if and only if the RMSD between the representative of the most similar cluster and the member is below a user specified RMSD threshold Otherwise a new cluster is created and the member is assigned to be the cluster representative 4 The clustering procedure is terminated when the total number of clusters created exceeds Max number of poses returned user defined molegro virtual docker user manual 22 Appendix V Clustering Algorithm page 212 251 parameter or when all members of the pool have been assigned to a cluster 5 When the cluster procedure has terminated the set of representatives one from each cluster is returned molegro virtual docker user manual 23 Appendix VI Supported File Formats MVD accepts the following molecular structure formats PDB Protein Data Bank Supported file extensions pdb ent a Mol2 Sybyl Mol2 format Supported file extensions mol2 a SDF MDL format Supported file extensions sdf sd for multiple structures and mol md for a single molecular structure Currently the following information is ignored during import of molecular structures a Lone pairs and dummy atoms all file formats a When alternative atoms are reported only the first alternative is used The remaind
177. l docker user manual 7 Analyzing the Docking Results page 113 251 Dynamic update Show hydrogen bonds Orient hydrogens to optimal position Show electrostatic interactions Display only residues closer than A 6 00 Show matching receptor configuration Re evaluation of poses Ranking Score coefficients unk MVD Misc Data RerankingCoefficients bt Recalculate Energies Pose Name The name of the ligand the pose was created from The file the pose was loaded from if any The workspace mvdmlfile containing the protein Evaluated before post processing only when using Plants The scoring function used by the GPU Screener Evaluated after post processing The reranking score arbitrary units The RMS deviation from a reference ligand f available The total interaction energy between the pose and the target molecule s The interaction energy between the pose and the cofactors The interaction energy between the pose and the protein The interaction enerav between the pose and the water molecules Add descriptor from regression model Figure 77 Pose Organizer settings The Dynamic Update Panel The top panel Dynamic update chooses how the Pose Organizer behaves when single pose selection Dynamic update is enabled It allows you to visualize hydrogen bonds electrostatic interactions orient hydrogens in the protein and ligand to their opti
178. lDock scoring function will always use unsoftened potentials The Docking Wizard will warn you if either of these requirements are not fulfilled When sidechain flexibility has been setup a sidechain flexibility description is added to the workspace This information is stored as part of the MVDML file molegro virtual docker user manual 8 Sidechain Flexibility page 132 251 In the Workspace Explorer a new category Flexible Residues will appear indicating that a sidechain flexibility description is present in the workspace 8 1 The Setup Sidechain Flexibility Dialog To invoke the Setup Sidechain Flexibility dialog select Docking Setup Sidechain Flexibility see Figure 87 If the workspace already contains a Sidechain flexibility description you can edit it by using the context menu on the Flexible Residues group in the Workspace Explorer and selecting Setup Sidechain Flexibility i lle 85 1 1HVR B 0 9 Add Closest to Active Ligand Add Visible Add Selected Clear List Remove selected Remove Non selected Adjust potential for selected sidechains Tolerance 0 90 Set to default Strength 7 00 _ Set to default 7 Set selected sidechains flexible during docking Figure 87 The Sidechain Flexibility dialog The Setup tab allows you to select a number of sidechains and define their individual properties that is how the potential should be soft
179. laced water interactions and styling of water molecules for visual inspection in the 3D visualization window Since the Ligand Energy Inspector is not aware of which scoring function settings were used during the docking run it is necessary to match the settings selected in the Docking Wizard or specified in the MVD script file Therefore the Displaceable water option needs to be toggled on in the Settings tab see Figure 92 Also if any entropy reward was applied during docking the same reward value should be specified in the Entropy reward for each water displaced setting Afterwards to update the energy contributions listed in the other tab pages the ligand needs to be re evaluated by pressing the Re evaluate button molegro virtual docker user manual 9 Displaceable Water page 144 251 Ligand pose H3151 Hide other ligands poses Ligand l Targets Total Energy Settings Scoring function MolDock Score Ligand evaluation E Intemal ES E Intemal HBond no directionality Sp2 Sp2 torsions Displaceable water evaluation E Displaceable water Entropy reward for each water displaced 0 00 Hydrogen bond evaluation V Hydrogen positions are optimized Optimize ligand and protein hydrogen positions using the Action menu before enabling this option Copy tables to clipboard Figure 92 Ligand Energy Inspector Re evaluating displaceable water interactions When the ligand h
180. lated The topological distance is the minimum number of covalent bonds connecting two atoms This way we can extract a list of the topological distance between any two pairs of chemical classes For instance we will have a list of distances between any atom from the HD class to any atom in the HA class molegro virtual docker user manual 14 Molecular Descriptor Calculations page 177 251 R Hydrogen ae Acceptor v Hydrogen 7 4 5 Donor ay Figure 114 CFDM Calculation the atoms in the molecule are assigned to one or more classes such as ring atom or hydrogen donor Then all topological distances the minimum number of covalent bonds between any two classes are measured For instance the minimum distance between the hydrogen acceptor atom and one of the hydrogen donor atoms is 5 as indicated on the figure This information is summarized in a number of matrices This information may be summarized in a number of distance matrices We can construct a matrix with minimum distances between any two classes a matrix with mean distances and a matrix with maximum distances HD HA POS NEG RING nem 3 5 0 0 1 HA 0 0 0 1 POS 0 0 0 NEG 0 0 RING 2 Table 2 Example of distance matrix This way we end up a total of x Nx N 1 2 numbers where N is number of chemical classes included per default 5 HD HA POS NEG and RING and molegro virtual docker user ma
181. le regions Notice that polar atoms capable of making hydrogen bonds would be allowed to be closer to the protein The tab serves two purposes a Visualizing the effects of softening the potentials or Comparing the potentials of two different receptors This can be useful if you have several different crystallographic structures and want to compare them in order to determine how the receptor potential should be softened molegro virtual docker user manual 8 Sidechain Flexibility page 136 251 gL Sidechain Flexibility Sets p Visualize Show frame 0 1 Compare potential before and after softening Compare two different structures First Conformation Second Conformation LJ Cofactors 0 2 LJ Cofactors 0 2 Proteins 2 2 H Proteins 2 2 Poses 0 5 H O Poses 0 5 a O Ligands 0 2 w O Ligands 0 2 Figure 89 The Sidechain Flexibility visualization tab In order to visualize the effects of softening the potentials first setup a search space the surface grids will only be drawn for molecules inside the search space If a search space has not already been defined you can use the Search Space button on the main toolbar to define one When pressing Create Animation 20 wireframe energy contour surfaces will be created In order to inspect the surfaces view the animation use the slider located at the top of the dialog Show frame x x After having ins
182. le to use a single card at a time If you have more than two CUDA devices installed it is necessary to choose the required device The default device may be selected from the preferences in MVD Select Edit Preferences and on the General tab choose the number of the required default CUDA device a list of the detected CUDA devices and their corresponding IDs may be found by choosing Help Show Available CUDA Devices The default device specified in the program preferences is used unless anything else is specified It is possible to override the default device settings by either molegro virtual docker user manual 6 Docking Functionality page 107 251 Specifying a CUDA device as a command line parameter when starting Molegro Virtual Docker This is done using the cudadevice parameter e g MVD exe cudadevice 1 where the number refers to the indices as listed above In a mvdscript specify the desired device using the CUDADEVICE command e g in a script add the following line before the dock and optimizer command CUDADEVICE 1 OPTIMIZER populationsize 50 cavity true LOAD Unnamed _complex mvdml DOCK Setting up a GPU Screening run In order to set up a GPU Screening run prepare the workspace as for a normal docking simulation and start the Docking Wizard Now go to the Customize Search Algorithm and set the algorithm to GPU Screening CUDA BY Docking Wizard Search
183. lecules and remove all irrelevant water molecules from the workspace before starting the docking run waters can be easily removed using the crop option in the Hides Residues dialog Example re docking the ligand from 1STP available in examples folder including six relevant water molecules is approximately twice as slow when enabling displaceable water evaluation compared with default settings Taking all water molecules into account makes the displaceable water evaluation eight times slower than docking with default settings The overall strategy when evaluating a given ligand conformation is to inspect each water molecule individually and decide whether or not it interacts favorably with the ligand Favorable water molecules are kept whereas non favorable water molecules are displaced or ignored The next section describes this evaluation procedure in more details The displaceable water evaluation in MVD consists of two main steps The first step is to pre calculate energy interactions between a water molecule and all protein and cofactor heavy atoms Ewater protein cofactor ANd between a water molecule and all other water molecules Ewater other waters Both Ewater protein cofactor and Ewater other waters Contributions are calculated using the MolDock scoring function see Appendix I MolDock Scoring Function for details Notice the Evwater other waters interactions are pre calculated and include all water molecules in the workspace In
184. legro Virtual Docker comes with a model trained to predict binding affinities The model is located in Misc Data BindingAffinity mdm The coefficients for molegro virtual docker user manual 7 Analyzing the Docking Results page 115 251 the binding affinity terms were derived using multiple linear regression The model was calibrated using a data set of more than 200 structurally diverse complexes take from the PDB data bank with known binding affinities expressed in kJ mol The Pearson correlation coefficient was 0 60 when doing 10 fold cross validation It is important to note that this particular model was trained only on strongly interacting ligands in their optimal conformation known from the PDB complexes Since the binding affinity measure was trained using known binding modes only it might sometimes assign too strong binding affinities to weakly or non binding molecules false positives We therefore recommend ranking the results of a virtual screening run using the rerank score The binding affinity measure may then be used subsequently to get a rough estimate of the highest ranked poses In order to inspect the BindingAffinity mdm model import the model into Molegro Data Modeller File Import Workspace Dataset Models The model then appears in the workspace By right clicking the model and selecting Show Details and choosing the Model tab it is possible to see the actual multiple linear regression exp
185. les its time when multiple processes are running simultaneously Per default Molegro Virtual Grid runs processes with below normal priority This means that when running other applications on a machine with a running agent the other applications get more CPU time resulting in a more responsive system It is also possible to set the priority even lower to lowest idle for instance to make it possible to run the agent on a desktop computer which is also used for normal work the running jobs will only get CPU time when no processes request it Notice that we strongly recommend against setting the priority higher than 0 The jobs will most likely not run faster but might instead make the operating system unresponsive The following values are available 10 highest real time 0 normal 1 below normal 10 lowest idle Notice that different OS s may use other process priority values internally The values are translated by the Virtual Grid agent so 10 is always the lowest priority no matter what OS the agent is running on molegro virtual docker user manual 15 Molegro Virtual Grid page 185 251 maxthreads The maxthreads options determines the maximum number of simultaneous instances of MVD spawned by the agent Under most circumstances is not necessary to set this value This number is per default set to the number of physical CPU cores In some cases it might be useful to limit the number of threads fo
186. license more details about licensing can be found in Section 15 3 and Section 15 10 We have designed Molegro Virtual Grid to be as easy as possible to install and operate However as with all networked software it is important to understand a few things about network security and firewall setup Data is transferred unencrypted between the agent and the controller This means that sensitive molecular data should never be transferred on the internet since it is possible to intercept the data The Molegro Virtual Grid infrastructure is designed for a trusted private intranet network If both your controllers and agents IP numbers are in the range 10 0 0 0 10 255 255 255 172 16 0 0 172 31 255 255 or 192 168 0 0 192 168 255 255 you are using a private network If you need to connect to Molegro Virtual Grid on another private network or over the internet we strongly suggest using VPN to secure the connection most likely this is already a requirement for accessing the private network If you are in doubt whether your network is safe to use please contact your network administrator Molegro Virtual Grid use unencrypted traffic over TCP UDP Port 45454 Molegro Virtual Grid automatically tries to detect other machines on the local network This is done using UDP pings If you are connecting to another network or using VPN UDP might be blocked In this case it is necessary to specify the IP numbers or DNS names of the machines that make up
187. llows you to activate a preset view by pressing the Select button or delete a view the Delete button Notice that when deleting a view you are not able to recover it unless you restore all macros this can be done by choosing Edit Macro and Menu Editor and pressing Restore all macros but notice that all user changes to the macros will be lost Style and Color Rendering Interactions Preset views Reset View Hydrogen Bond Interactions Docking View Preparation View Hydrophobicity Electrostatic Interactions Pose Organizer View Secondary Structure View Macro based on current settings Visualization Settings style ligand vdw 0 2 0 05 style pose vdw 0 2 0 05 style protein wireframe 0 15 0 152 style water wireframe 0 15 0 152 style cofactor vdw 0 2 0 05 Color settings asalarliansnd anle Use as Default Settings Restore Default Settings to Factory Settings Restore to Default Settings Figure 44 The Visualization Settings Views tab The lower panel allows you to create new views based on the current visualization settings By pressing New View a dialog allows you to specify the name for the new view after which it is added to the list of views on the main window menu bar Views are stored as parts of the macros xml file and appear under the View menu item It is also possible to modify the macro in the text area before committing it as a macro Modified macro
188. lowing file formats a Protein Data Bank pdb ent a Sybyl Mol2 mol2 a MDL sdf sd mol mdl Notice that only PDB and Mol2 files can contain proteins and water molecules In general it is recommended to use Mol2 or SDF files for ligands since they can contain bonding information From the Import Molecules dialog shown in Figure 53 it is possible to select which molecules to import prepare molecules and inspect warnings found during parsing of the imported file Notice If more than 10 ligands are present in the file typically SDF or Mol2 files a subset of the ligands can be selected for import using the Specify ligand range option see Figure 53 Since it is computationally slow to display a large number of molecules e g thousands of compounds ligands and poses are not automatically shown in the Visualization Window if the number of molecules imported exceeds 50 for each category molegro virtual docker user manual 4 Preparation page 68 251 impot Preparation ZN Warnings n Select which molecules to import 1_LIG 41 atoms ZINC03775575 68 atoms ZINCO0006989 40 atoms ZINC03776578 56 atoms ZINC00016193 19 atoms ZINC03778899 75 atoms ZINC00597437 56 atoms ZINC03779042 32 atoms ZINC03780014 56 atoms ZINC03780893 68 atoms ZINC01536875 65 atoms ZINCO1534489 54 atoms ZINC01530558 24 atoms ZINC03783756 63 atoms ZINC00585151 56 atoms stamoal L M inien270c191 190 Spec
189. lows you to add explicit hydrogens based on the implicit ones Creates hydrogens matching the predicted number of hydrogens in the step above The hydrogens are placed according to geometric criteria i e SP3 hybridized atoms are kept at a 109 degrees geometry The hydrogens are placed at standard distances according to the atom they are connected to No energy minimization is performed This option allows to assign partial charges to each atom based on the scheme described in Appendix I MolDock Scoring Function This option determines which bonds that should be considered flexible during docking It is advisable always to set this option to either If Missing or molegro virtual docker user manual 4 Preparation page 71 251 Always If this option is set to Remove the ligand will be considered rigid during docking This option is used to assign Tripos atom types using a built in heuristic If the option is set to Never atom types will be imported from the molecule file instead of being assigned by MVD only available for Mol2 structural files The Remove option will set all atom types to Undefined Always will assign Tripos atom types to all atoms using built in assignment rules and If Missing default will assign atom types to Dummy Undefined and Other typed atoms using built in rules all other atom types will be imported from the Mol2 file Atom hydrogen bonding types acceptor donor both or non polar are always
190. ls in the last section Chemical Feature Distance Matrix Descriptors of this chapter The CFDM descriptors are obtained by calculating the minimum maximum and mean topological distance between all pairs of chemical features The topological distance is defined as the smallest number of covalent bonds between the two features The following chemical features are investigated hydrogen acceptors hydrogen donors positively and negatively charged atoms and ring systems Notice that a minimum charge of 0 2 is required for an atom to be considered charged this threshold may be changed in the settings dialog Wiener Index The Wiener Index is the sum of the topological distance between all heavy atom pairs molegro virtual docker user manual 14 Molecular Descriptor Calculations page 174 251 The final step is to choose an output format f Descriptor Calculation lt Back Stat Canca Figure 112 Choosing an output format The are two possibilities a Open In Molegro Data Modeller The resulting output is directly opened as a dataset in Molegro Data Modeller for further analysis a Save as CSV text file This will save the output as a tab separated text file This kind of output can be read by virtually all data processing software products There are several potential uses for molecular descriptors Molecular descriptors can be used to quickly screen a molecule library for compo
191. lso possible to search in atom coordinates by prepending the search with a e g searching for 1 23 will return atoms where one of the coordinates starts with 1 23 By default the Fit to screen option is enabled so that items molecules residues or atoms are fitted to the Visualization Window while browsing the list of results found The Fit to screen option can be disabled in the options panel invoked by pressing the small button on the right hand side of the Workspace Finder search box The Sequence Viewer dialog see Figure 26 allows you to inspect protein residues in an easy manner The dialog can be invoked by selecting Window Sequence Viewer or using the Ctrl Shift S keyboard shortcut Using the context menu on the Sequence Viewer window it is possible to molegro virtual docker user manual 3 User Interface page 36 251 select residue atoms in the Visualization Window hide non selected residues change between one and three letter residue names and toggle details about secondary structure Residues near cavities are indicated with a green ribbon the distance threshold may be set using the sequence viewer s context menu and broken protein chains are indicated with vertical lines between residue endpoints Detailed information about residue name index and secondary structure assignment is available in the tool tip which can be invoked by focusing the mouse on a specific residue in the Sequence Viewer
192. mal position and dynamically show residues close to the chosen pose The Orient hydrogens to optimal position option is useful when inspecting poses as this makes it easier to see if the hydrogen bond is optimal Working with Receptor Conformations When docking with sidechain flexibility a receptor conformation is saved together with each pose When a new docking results file is imported MVD molegro virtual docker user manual 7 Analyzing the Docking Results page 114 251 automatically checks whether any receptorConfiguration files exist together with the poses If this is the case the option show matching receptor configuration under dynamic update is enabled When in dynamic update mode the pose organizer will now automatically change to the receptor conformation corresponding to the selected pose If poses are imported into the workspace their corresponding receptor conformations will automatically be added to the workspace The middle panel allows for recalculation of the MolDock Score and re ranking score terms These scoring function values are already calculated if the poses are imported from a mvdresults file Pressing the Recalculate Energies button will recalculate the energy terms using the coefficients specified in the file for the re ranking scores Notice that the default evaluator settings will be used e g internal ligand hydrogen bonds are not enabled The reranking score function is computationally more exp
193. molegro virtual docker page 2 251 ll bio Molegro A CLC bio company Copyright 2005 2013 Molegro A CLC bio company All rights reserved Molegro Virtual Docker MVD Molegro Data Modeller MDM Molegro Virtual Grid MVG and MolDock are trademarks of CLC bio All other trademarks mentioned in this user manual are the property of their respective owners All trademarks are acknowledged Information in this document is subject to change without notice and is provided as is with no warranty CLC bio makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose CLC bio shall not be liable for errors contained herein or for any direct indirect special incidental or consequential damages in connection with the use of this material molegro virtual docker user manual page 3 251 Table of Contents 1 Introduction to Molegro Virtual DOCKES cccccceee eect eee ee ee eeneeeeeaneeeenaaenes 7 1 1 CONTACT Informatiounen severe tev dsecter lee iedsdeeaesddebinedd Mieeiions 8 1 2 System Requirements suscts tutdasusttacwedudssberuguad ude enaiaeraserideuseiwens 8 1 3 Reporting Program EMP Or sie cecicinctuisunscidnausetnnewseceaendeiaxeeeeixcunsed Ea 8 1 4 Text Formats Used in the Manual icccticias soessestrussenininsesdoteveesesetocicvesonta 9 1 5 Keyboard SMO CUS sisipin aa ieee ereseeieredeea deers 9
194. mount of information that will be saved to the time stamped log files created during the docking simulations In particular the None and Errors options are suitable for virtual screening runs since the amount of information saved will be small The setting is used for all docking runs started on the local machine where MVD is installed T ca Preferences i Graphies Mouse Parsing Load most recent workspace on startup if any Show tip of the day on startup 7 Check for new updates on startup Ligand Energy Inspector auto optimizes hydrogens 7 Create system log in directory below System log directory requires restart cuments MVD Data Logs Working directory C Users Mikael Documents MVD Data Virtual Grid executable n Files Molegro MVD bin wirtualgnd exe PDF viewer CUDA device 0 H Level of details for docking file logs Reset All to Defaults Figure 104 General preference settings The Graphics tab see Figure 105 contains settings related to the Visualization Window molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 159 251 i Preferences i Mouse Parsing F Show pivot point rotational center Default E Show root atom Default T Fade 3D labels when in background Default Quality 10 la Default Notice to change the default visualization styles
195. n 12 02 44 170 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 04 1 12 02 44 171 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 Unit 2 12 02 44 172 Sending Job Unit 3 to agent 192 168 1 152 ID 82d449ad 09f7 4597 b101 7a9f7710148e 12 02 44 174 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 Unit 3 12 02 44 176 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 01 1 12 02 44 177 Removed previous results F WorkingDir 2480a911 cdeb 4 aa8 bOf7 50cfed28abd7 02 1 12 02 44 178 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 03 1 12 02 44 179 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 04 1 12 02 44 180 Removed previous results F WorkingDir 2480a911 cdeb 4aa8 bOf7 50cfed28abd7 Unit 3 Log window l Toggle log Minimize to System Tray Figure 118 The Molegro Virtual Grid Controller GUI On Figure 118 the left panel shows a list of the agents that are currently available for processing job units If Auto Discover is enabled this list will be automatically populated with agents that can be recognized on the local network Not all network and firewall configurations allow automatic discovery of agents in this case it is necessary to manually add agents this is done using
196. n used while docking lt type gt is one of the following values MolDockGrid for the grid version of the MolDock evaluator MolDock for the standard version of the MolDock evaluator PlantsGrid for the grid version of the PLANTS evaluator Plants for the standard version of the PLANTS evaluator Ligand for an evaluator only taking the ligands internal energy into acoount for when docking with templates Notice MolDock is set automatically as the default evaluator Example EVALUATORTYPE MolDockGrid MKDIR lt path gt Creates a new directory molegro virtual docker user manual 28 Appendix XI Script Commands page 233 251 OPTIMIZER lt initstring gt Sets the settings for the optimizer the docking search algorithm The lt initstring gt is semi colon separated string of parameter value pairs The following parameters are available Their default setting is marked in bold For more information about the parameters see Appendix III MolDock Optimizer Appendix XII MolDock SE Appendix XIII Iterated Simplex or the Docking Wizard section where some of the parameters are described popsize integer 50 Determines the number of individuals in the population cavity true false Determines whether poses should be forced to be in cavities randomizeligand true false Determines whether the ligand orientation should be randomized before each docking run
197. n is able to more precisely take hydrogen bonding geometries into account Enabling this option will usually result in very tiny improvements and the option is disabled by default Optimize H Bonds optimizes the position of the hydrogens for any hydrogen donors both in the Ligand and in the Proteins The default behavior for the MolDock score is to only evaluate hydrogen bond angle geometry for hydrogen bonds where the hydrogen positions are fixed non rotatable By optimizing both protein and ligand positions first additional geometric constraints can be used to evaluate the quality of a hydrogen bond Notice that enabling this will always slightly raise the energy since the geometric hydrogen bond terms are penalties imposed on the hydrogen bond energies this does not mean that the solution is worse after optimizing the hydrogen bonds but rather that the more accurate evaluation has made it possible to impose additional penalties on the hydrogen bonding geometry By default h bond optimization is enabled Notice that the After Docking settings become unavailable if the workspace contains docking templates sidechain flexibility descriptors or constraints Notice For large ligands with more than 10 15 flexible bonds 20 50 runs are sometimes needed Using the MolDock SE search algorithm and the grid based version of the docking scoring function can reduce the computational load significantly good results have been reported using this combina
198. nal strain Torsional strain sp2 sp2 Hydrogen bonds Steric by PLP srin me Copy tables to clipboard Figure 94 Energy contributions from various terms including the Displaceable Water Interactions For a more visual inspection of the displaced and non displaced water molecules it is possible to style the water atoms based on their individual energy contributions This styling can be enabled by selecting the Style Water Atoms by Energy option from the Action menu The radius of the water atoms will be scaled proportionally to their energy contributions and displaced waters are colored yellow non displaced waters are colored green if they are favorable and red if they are not favorable Figure 95 shows an example of the Style Waters by Energy visualization style Notice that the styling is not updated automatically so whenever a ligand is re evaluated using the Re evaluate button located in the Settings tab the action has to be selected again from the Action menu to update the visualization view molegro virtual docker user manual 9 Displaceable Water page 147 251 Figure 95 Example of Style Waters by Energy action The green spheres represent favorable non displaced water molecules and the yellow sphere represents a displaced water molecule molegro virtual docker user manual 10 Template Docking Template docking can be used when knowledge about the 3D c
199. nal term for the pose Notice This is a non standard term and is zero by default it must be enabled by specifying the sp2sp2bond true option to the EVALUATOR initializer list in a MVDScript file or by enabling the Sp2 Sp2 Torsions option in the Docking Wizard Also notice that only bonds that are chosen rotatable are taken into account when calculating the torsional terms for the ligand and sp2 sp2 bonds are most often double bonds which per default are held fixed in the docking simulation E Intra vdw Steric self interaction energy for the pose calculated by a LJ12 6 VdW approximation Notice This term is not used by the MolDock score E Solvation The energy calculated from the implicit solvation model Notice This energy term is considered to be an experimental feature only Per default it is NOT calculated In order to try this feature the protein must be prepared by calling the prep solvation command from the console As of now we recommend not to use it E Soft Constraint Penalty The energy contributions from soft constraints Static terms Torsions The number of chosen rotatable bonds in the ligand HeavyAtoms Number of heavy atoms MW Molecular weight in dalton co Obsolete constant term This value is always 1 Older versions of the Data Analyser required an explicit constant column in order to include a constant term in the fit it is only included fo
200. nformations are available in the workspace a drop down box will appear at the bottom of the Workspace Explorer allowing the user to molegro virtual docker user manual 3 User Interface page 28 251 change between conformations For more information about working with multiple receptor conformations see Chapter 8 rro pi A V The Properties Window contains information about the currently selected or highlighted 3D object s in the Visualization Window and provides useful information while preparing and modifying the molecules Figure 19 shows an example of different properties for a highlighted atom Properties Property Value Selection Position 11 156 14 282 34 709 Atom ID Element PDE atom name PDE atom ID Tripos atom type C ar Plants atom name Not Defined Hydrogens 1 Ydw radius 174 Covalent radius 0 684 Hydrogen bonding Nonpolar Partial charge 0 Hybridization Sp2 Temperature 29 56 Average angle 120 Clear Selection Figure 19 Example of properties for a selected atom The Visualization Window see Figure 20 visualizes all the selected molecules in the workspace and all custom graphical objects e g labels annotations charges protonation guides backbones surfaces and cavities Notice For large molecules it can be computationally slow to display all atoms Therefore it is recommended to adjust the view to the user s needs Often it is a good idea to add a molecular surface perhaps tra
201. ng a water molecule only applies when the DisplaceWater option is enabled The following parameters are available to MolDock Score and MolDock Score Grid molegro virtual docker user manual 28 Appendix XI Script Commands page 231 251 EVALUATOR lt initstring gt ligandes true false Determines whether the internal electro static energy of the ligand should be included internalhbond true false Determines whether internal hydrogen bonds in the ligand are allowed torsion first mean all Determines how torsion terms are evaluated if several torsion angles are available for a bond sp2sp2bond true false Determines if sp2 sp2 bonds should be taken into account eintra true false Determines whether ligand self interaction energy should be taken into account skiptorsionterm true false Determines whether ligand torsions are taken into account hbond90 true false Determines whether hydrogen bonding directionality should be taken into account Notice The hbond90 option is not available for the grid evaluator or for the PLANTS scoring functions The following parameters are available to PLANTS Score and PLANTS Score Grid ignorehtors true false toggles whether or not hydrogens should be included when calculating the Tripos torsion potential Originalplants true false toggles between original Plants setup using PLANTS specific binding penalty terms and ign
202. ng a web interface see below molegro virtual docker user manual 15 Molegro Virtual Grid page 182 251 15 5 The Agent GUI Working directory F WorkingDir Units Unit ID 0 status WaitingForFiles 0 Owner Molegro Test Controller ID 2480a911 c Unit ID 1 status WaitingForFiles 0 Owner Molegro Test Controller ID 2480a911 c Time Description 11 52 56 065 Job Unit 7 completed Returned files F WorkingDir 24802911 11 53 00 880 Job Unit 8 completed Returned files F WorkingDir 2480a911 12 02 13 951 Deleting files in F WorkingDir 2480a911 cdeb 4aa8 b0f7 50 12 02 13 990 Received Reset All signal Killed 0 running processes Remove 12 02 44 219 Creating dir 2480a911 cdeb 4aa8 b0f7 50cfed28abd7 in dir 12 02 45 544 Job Unit 2 started 4 available 0 pending 12 02 45 916 Job Unit 3 started 3 available 0 pending 12 03 22 011 Job Unit 3 completed Returned files F WorkingDir 2480a911 12 03 25 111 Job Unit 4 started 3 available 0 pending gt Log window Agent P 2 PR 0 A 2 82d449ad 0947 4597 b101 Toggle log Minimize to System Tray Figure 116 The Virtual Grid Agent GUI In order for the agent to execute docking runs it must know the location of the MVD executable Either type a location in the MVD path settings box or browse to the location using the button If you manually type
203. ns will be indicated visually in the workspace as wireframe spheres The sphere color will depend on the strength parameter and the sphere size will reflect the tolerance parameter see Figure 88 molegro virtual docker user manual 8 Sidechain Flexibility page 135 251 Witpmami Molegro Virtual Docke File Edit View Rendering Preparation Docking Tools Window Help S Q ir w v Hydrogens Fog Hide Residues al items Options v 5 Workspace New Cavities 1 F Constraints 1 oai 4 VI Flexible Residues 2 M Sera 4 M Ligands 1 4 Proteins 1 Water 84 Property Value Selected Atoms 2 Non bonded atoms Distance 6 17548 l Clear Selection Figure 88 Visualization of flexibility descriptors Sidechain flexibility descriptors are saved as part of the workspace The sidechain flexibility description is read and used directly by the docking engine see the section Sidechain Flexibility in the Docking Wizard for information about setting up a docking run with sidechain flexibility The Visualization tab Figure 89 is used to create small animations showing wireframe surfaces interpolating between two different potential energy landscapes The wireframe surfaces are determined by probing a receptor energy grid with a carbon atom The grid surface marks the boundary between energetically favorable and non favorab
204. nsparent to give some idea of the 3D structure Alternatively switching to wireframe visualization style and hiding non polar or all hydrogens atoms can also improve the visualization speed significantly Also consider cropping removing non relevant parts of the complex in order to make the visualization faster Cropping is described in Section 3 9 molegro virtual docker user manual 3 User Interface page 29 251 Changing the 3D World Appearance The visualization engine is highly configurable Molecules can be drawn as lines wireframe ball and sticks capped sticks and space fill CPK File Edit View Rendering Preparation Docking Tools Window Help j B Jap Em As Q a i Hydrogens Fog Hide Residues E Workspace New O Cavities 1 O Constraints 1 Ligands 1 O Proteins 1 Surfaces 1 C Water 84 sie Ss sp cs a Done processing macro Figure 20 Visualization of Biotin 1STP in capped stick style and electrostatic protein surface Notice Ball and stick is the preferred style for handling preparation of ligands since the visualized bond shows bond order and is color coded to display whether the bond is set rigid brown or red or flexible green molegro virtual docker user manual ke Istp mvdmi Molegro Virtual Docker File Edit View Rendering Preparation Docking Tools Window Help E3 w SA E v v Hydrogens v Fog Hide Residue
205. nstraints Distance constraints constrain ligand atoms to a given position in 3D space see Figure 62 They are used to constrain some or all atoms of a ligand to the vicinity of this position Distance constraints are visualized as an inner and outer sphere where some ligand atoms must be present between the spheres Y 13 40 Z 18 40 Specific ligand atomid 0 Ligand atoms of type All Specific atoms for each ligand Define from selected atoms View list Require distance to be between Minimum 2 30 Madmum 3 60 Penalize distances with Piecewise Linear Potential term Energy penalty AO 20 00 Al 2 50 gt Distances A RO 2 30 R1 2 60 R2 3 10 R3 3 60 Figure 62 The Distance Constraint dialog The Distance Constraint dialog can be invoked either via the context menu on an atom Create Distance Constraint or by selecting one or more atoms and using the context menu option Set Selection as Center of molegro virtual docker user manual 6 Docking Functionality page 89 251 Distance Constraint If several atoms are chosen their mean position will be set as center for the constraint The top panel allows the user to modify the location of the constraint Constraint Center It also controls which parts of the ligand should be constrained Either a single atom the Specific Ligand Atom ID option or multiple atoms the Ligand Atoms of Type drop
206. ntaining the protein Filename The file the pose is stored as only available when inspecting docking results from a mvdresults file MolDock Score Evaluated after post processing This is the Energy term in a mvdresults file Rerank Score The reranking score arbitrary units Plants Score Evaluated before post processing only when using Plants This is the PlantsScore term in a mvdresults file RMSD The RMS deviation from a reference ligand if available Interaction The total interaction energy between the pose and the target molecule s This is the E Inter total term in a mvdresults file Cofactor The interaction energy between the pose and the cofactors This is the E Inter cofactor ligand term in a mvdresults file Protein The interaction energy between the pose and the protein This is the E Inter protein ligand term in a mvdresults file Water The interaction energy between the pose and the water molecules This is the E Inter water ligand term in a mvdresults file Internal The internal energy of the pose This is the E Intra tors ligand atoms term in a mvdresults file Torsions The number of chosen rotatable bonds in the pose Soft Constraints The energy contributions from soft constraints This is the E Soft Constraint Penalty term in a mvdresults file Electro Short range electrostatic protein ligand interations r
207. nual 14 Molecular Descriptor Calculations page 178 251 M is the number of matrices per default 3 MIN MEAN and MAX giving a default of 45 descriptors The organization of the descriptors into matrices is purely conceptual they will be output as 45 numbers in a row vector Settings for CFDM Descr otor Chemical Features 7 Calculate minimum topological distance MIN V Calculate average topological distance MEAN 7 Calculate maximum topological distance MAX Calculate sum of topological distances SUM Reset All to Defaults Apply Figure 115 Choosing which matrices to include Finally the descriptors are named using the following convention for instance HA POS MEAN means the mean topological distance between any HA and POS atom molegro virtual docker user manual 15 Molegro Virtual Grid Molegro Virtual Grid is a framework for distributing docking runs It can be used for running large jobs on multiple machines in a network or for running smaller jobs using all the available cores on a single machine The Virtual Grid consists of two components The Controller is a graphical application which loads a job description and distributes the individual job units to the available resources The controller is also able to retrieve combine and filter the resulting data The Agent is a small lightweight application that runs in the background and listens for work re
208. ocker user manual 24 Appendix VII Automatic Preparation page 216 251 a Lastly the geometry surrounding a SP2 atom should be planar otherwise it is degraded to SP3 a All atom bonds are set to unknown All implicit hydrogens are set to 1 a All bonds to SP3 atoms are set to single order a Next a template file containing standard chemical motifs POO C NH2 NH2 is processed The templates are located in the file misc data preparationTemplates xml a All unset SP2 SP2 bonds involved in a planar geometry less than 10 degrees are set to double a Next all SP2 atoms are checked to see if a double bond to a neighbour atom is possible If several atom bonds are possible the atom with highest electro negativity is chosen If this still results in several possibilities the atom closest to the current one will be chosen molegro virtual docker user manual 25 Appendix VIII Third Party Copyrights MVD uses a derivate of the MD5 hash algorithm RSA Data Security Inc MD5 Message Digest Algorithm under the following license You may use this software free of any charge but without any warranty or implied warranty provided that you follow the terms of the original RSA copyright listed below Original RSA Data Security Inc Copyright notice Copyright C 1991 2 RSA Data Security Inc Created 1991 All rights reserved License to copy and use this software is granted provided that it is i
209. ocking Results page 129 251 threshold will be displayed in the statusbar of the main window when adjusting the sliders Notice that for steric interactions only non favorable interactions clashes are shown showing the numerous positive interactions would clutter the interaction diagram However by placing the mouse cursor over an atom or residue the favorable steric interactions will also be shown It is also possible to visualize how much each ligand atom contributes to the overall binding interaction By clicking Interaction Overlay a sphere centered at each atom visualizes the strength of the interactions for this specific atom By enabling the Hide Residues option it is possible to hide residues in the 3D visualization window that are not shown in the 2D Ligand Map The Redo Layout button makes it possible to calculate a new layout for the molecule and its interactions for instance if the layout contains clashing bonds It is possible to zoom in and out using either the mouse wheel or the zoom buttons in the lower right corner of the window Dac 7 Bq JACA M A eli fiar 5 Pose Modifier It is possible manually to modify a ligand or a pose found by right clicking the molecule in the Workspace Explorer and selecting Modify Pose see Figure 85 When invoking the Pose Modifier a new pose is created amp Pose Modifier Energy 183 948 Position 1 0 9 Position 2 0 Position 3 0 RotVector 1 1 RotVec
210. olDock SE algorithm simplexdistancefactor double Default is 1 0 This factor determines how close the point of the initial simplex will be to the other randomly selected individuals in the population A factor of 1 0 causes the initial simplex to span the neighbour points exactly while a factor of 0 5 would correspond to simplex points being created halfway between the individuals chosen for optimization and its randomly chosen neighbours Notice that a factor less than 1 0 will converge slowly Typical values should be in the range of 0 95 to 3 0 recombine true false Allows for turning off the Simplex Evolution phase The following parameters are used by the Iterated Simplex algorithm maxsimplexsteps int 2000 Maximum number of steps in Simplex local search performed for each individual simplextolerance double 0 01 The tolerance threshold used to terminate Simplex local search when refining an individual simplextolerancebest double 0 0001 The tolerance threshold used to terminate Simplex local search when refining the best found individual in the current iteration usepheromones true false Allows for turning on adaptive sampling using Ant Colony Optimization diversify true false Allows for turning on search diversification strategy see KORB 2009 for details pbest double 0 5 Probability of best individual Used by Min Max strategy for updating pheromone limits see KORB 2009 for details
211. olutionary Programming 1995 615 627 GEHLHAAR 1998 Gehlhaar D K Bouzida D Rejto P A Fully Automated And Rapid Flexible Docking of Inhibitors Covalently Bound to Serine Proteases Proceedings of the Seventh International Conference on Evolutionary Programming 1998 449 461 YANG 2004 Yang J M Chen C C GEMDOCK A Generic Evolutionary Method for Molecular Docking Proteins 2004 55 288 304 MCDONALD 1994 McDonald I K Thornton J M Satisfying Hydrogen Bonding Potential in Proteins J Mol Biol 1994 238 777 793 MICHALEWICZ 1992 Michalewicz Z Genetic Algorithms Data Structures Evolution Programs Springer Verlag Berlin 1992 MICHALEWICZ 2000 Michalewicz Z Fogel D B How to Solve It Modern Heuristics Springer Verlag Berlin 2000 STORN 1995 Storn R Price K Differential Evolution A Simple And Efficient Adaptive Scheme for Global Optimization over Continuous Spaces Tech report International Computer Science Institute Berkley 1995 SHOEMAKE 1992 Shoemake K Uniform Random Rotations In Graphics Gems III ist ed Kirk D Ed AP Professional Academic Press Boston 1992 pp 124 132 molegro virtual docker user manual 32 Appendix XVI References page 251 251 HAYKIN 1999 Haykin S Neural Networks A Comprehensive Foundation Prentice Hall Inc New Jersey 1999 SELWOOD 1990 Selwood D L Livingstone D J Comley J C W O Dowd A B Hudson A
212. onds Create explicit hydrogens Assign charges calculated by MVD Detect flexible torsions in ligands Assign Tripos atom types Notice The preparation options If Missing Aways Never Remove applies to each individual molecule not each individual bond or atom For instance setting Assign bonds to if Missing results in covalent bonds being created for molecules not containing any bonds at all while molecules with bond information will preserve their bond assignments Likewise setting Create explicit hydrogens to if Missing will not add additional hydrogens to molecules containing e g polar hydrogens onl In this case Alwavs should he used if all ltt a Figure 54 Preparing molecules Within all preparation types the following four different possibilities are available see Figure 54 a Always Unconditionally performs the preparation by MVD a Never Skips the preparation a If Missing The preparation will only be performed if no knowledge is already present e g if bond orders exist in the Mol2 file bond orders are not assigned by MVD However if bond order information is not included MVD will assign it a Remove Tries to remove preparation e g if Assign bond orders is set to remove all bond orders will be set to single bonds If Create explicit hydrogens is set to remove all hydrogen atom are removed molegro virtual docker user manual 4 P
213. onformation of a ligand is available For instance a protein might have one or more inhibitors with experimentally known 3D structures From the known conformations it is possible to create a template with features expected to be relevant for the binding This allows the docking engine to focus the search on poses similar to the docking template Docking templates can be used together with an ordinary docking scoring function in order to focus or guide the search but templates can also be used without any additional energy terms for instance if no structural information about the target is known This is useful for aligning ligands by defining a template from one or more ligands as a reference template and other molecules can then be docked and aligned to the template Notice that template alignment takes the ligands flexibility into account The docking engine will try to find the optimal conformation of the ligand when fitting to the template It is also possible to align molecules and extract detailed information about the similarity based on the overlap from each individual template point This information can then be used in Molegro Data Modeller to create a regression model against some known empirical quantity 3D QSAR Templates are implemented as scoring functions rewarding poses similar to the specified pattern A template is a collection of template groups where each group represents a chemical feature for an atom e g h
214. onformational space Initially a population of conformations for the current ligand is created with the poses located on the grid points predicted by the cavity detection at least one atom of each pose is located on a grid point The size of the population is controlled by the Simultaneous evaluations parameter Notice that in order to properly utilise the GPU a reasonable number of poses must be processed in parallel usually the default value of 256 is sufficient but for higher end graphics cards it might be possible to increase the number without affecting performance After the initial population has been constructed each pose is being minimized using the Nelder Mead optimization technique The Max iterations parameter determines how many Nelder Mead minimization steps should be performed if the minimization of a pose fails to improve beyond a given threshold the pose is re initialized with a random configuration on the cavity grid The GPU Screening algorithm can be specified in a mvdscript using the OPTIMIZERTYPE command e g OPI OPI TIMIZ ERTYPE TIMIZ CUDA ER poses 256 steps 1500 reevaluate false Optionally if more than one cuda device is present in a machine the desired device may be specified before setting the optimizer type and starting the docking CUDADE molegro virtual docker user manual 6 Docking Functionality page 109 251 Because o
215. ore 2 poses Figure 14 Viewing multiple poses Turn off the original ligand and the search space sphere colored green in the 3D view window by clicking the Ligands and Constraints check boxes in the Workspace Explorer The poses in the Pose Organizer can be visualized by selecting them see Figure 14 molegro virtual docker user manual 2 Docking Tutorial page 23 251 By enabling the Dynamic update option we can inspect the individual poses one at a time single pose view mode Click on the poses on the list to have them visualized see Figure 15 Notice that hydrogen bonds are dynamically updated and shown when switching to a new pose v Figure 15 Viewing hydrogen bonds The Pose Organizer can also automatically rotate rotatable hydrogens like hydroxyl rotors in both the receptor and the ligand to their optimal position It can also be used to rerank the ligands using a rank score or view their energy contributions split up into different categories see Section 7 1 for more details This concludes the tutorial molegro virtual docker user manual 3 User Interface Molegro Virtual Docker is based on the notion of workspaces The workspace is the central component and represents all the information available to the user in terms of molecules proteins ligands cofactors water molecules and poses user defined constraints visualized as small spheres cavities visualized as a grid mesh and
216. oring entries with dummy Tripos atom types in Tripos torsion potential and MVD implementation of PLANTS score using another binding penalty term and including dummy Tripos atom types in Tripos torsion potential See Appendix II PLANTS Scoring Function for details about the different binding penalty terms available for the PLANTS scoring function The gridresolution option is only available to grid based evaluators gridresolution double Sets the grid spacing where the grid resolution is specified in Angstrom The SoftenPotential option is only available for the MolDock Score Grid SoftenPotential true false Default is false Allows you to soften the potential during docking adjust the treshold and molegro virtual docker user manual 28 Appendix XI Script Commands page 232 251 EVALUATOR lt initstring gt strength for the atomic pairwise potentials In order to enable softening the project MVDML file must contain a description of the softened sidechains This can be made by choosing Docking Setup Sidechain Flexibility in the GUI The default settings from the Docking Wizard will generate the following evaluator string EVALUATOR cropdistance 0 hbond90 true Notice an easy way to generate a Suitable initstring is to use the Docking Wizard to generate and save a generated script EVALUATORTYPE lt type gt The EVALUATORTYPE command set the evaluator scoring functio
217. ound poses will be stored in the output directory cok Figure 10 The Batchjob dialog molegro virtual docker user manual 2 Docking Tutorial page 19 251 Now we can begin the docking simulation by pressing the Start button The Molegro Virtual Docker Batchjob dialog appears showing the docking progress see Figure 11 Docker Batchiob Finished Batchjob started ma 27 aug 13 21 04 2012 Bapsed 00 03 26 Skip run Finish estimated 13 24 44 Remaining 00 00 14 l Working path C Users Mikael Documents MVD Data DockingOutput 228 Curent ligand 10 10runs psn 100 Log Poses curent ligand 10 Poses all 4 Graph Curent script Time Description 13 24 12 631 Source Ligand was randomized This will destroy its original orientation 13 24 12 633 Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStud 13 24 12 642 Reading 626 values 13 24 12 644 Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVD Visual Stud 13 24 12 674 Reading 2378 values 13 24 12 675 Reading bias file f SUBVERSION CHECKOUT Projects Trunk MVD MVDVisualStud 13 24 12 699 Reading 1868 values 13 24 12 701 We are docking from the current active ligand XK2_263 13 24 12 719 Cavity information found in workspace 13 24 12 720 Shared cavity grid found Reusing t 13 24 13 185 Iteration 10 Lowest Energy 49 9211 RMSD 6 18397 13 24 13 647 Iteration 20 Lowest Ener
218. pe Colors atoms according to hydrogen bonding properties donors are red acceptors green and atoms capable of both donating and accepting hydrogens are yellow Color By Partial Charge Colors according to electrostatic partial charge blue corresponds to positive charge red to negative charge The following can only be applied to proteins Color By Temperature B Factor The temperature factor is a molegro virtual docker user manual 3 User Interface page 52 251 measure of how much a given atom vibrates around its position in the crystal structure Notice that this information is not always present in PDB files and that it is sometimes used for other purposes The colors will be interpolated between blue for the minimum temperature and red for the maximum temperature a Color By Amino Acid Type Colors proteins according to their residue type Color By Shapely Residue Scheme Same as above with alternative colors a Color By Residue ID Colors according to residue ID rainbow effect a Color By Secondary Structure Colors according to secondary structure red for helices blue for strands and yellow for turns a Color By Hydrophobicity Residue atoms are colored according to the hydropathy index proposed by Kyle and Doolittle in 1982 see http en wikipedia org wiki Hydropathy_index for details Hydrophilic residues are colored red hydrophobic residues are colored blue The Rendering tab Figure 42
219. pected the energy changes the surfaces can be removed from the workspace by using the context menu on the Surfaces category in the Workspace Explorer Remove All Surfaces From Workspace If the Docking Wizard is invoked and the workspace contains a sidechain flexibility description a new page will appear in the wizard after the first page Figure 90 Sidechain Flexibility in the Docking Wizard The first option Soften potentials during the docking turns on the softening procedure for the potentials Notice that is necessary to use the MolDock Score Grid for potential softening to have any effect molegro virtual docker user manual 8 Sidechain Flexibility page 137 251 2 Docking Wizard A Receptor flexbility description has been found in the workspace Sidechain Hexibility Setup V Soften potentials during the docking 0 sidechain s set to a non standard tolerance 0 sidechain s set to a reduced strength V Minimize receptor for each found pose 2 sidechain s 2 torsional degrees of freedom marked for flexibility Max minimization steps for residues and ligand 2000 Max global minimization steps 2000 Figure 90 Sidechain Flexibility in the Docking Wizard The next option Minimize receptor for each found pose turns the post docking minimization step on for the best found solutions during the docking run First the flexible sidechains are reoriented taking the pose into account Afterwards
220. pendix XI Script Commands page 226 251 28 1 List of Script Commands Available It is possible to add comments to MVD script files using either for a one line comment or to span more line Notice Currently it is not possible to add comments after script commands Examples This is a one line comment This is a comment spanning more than one line which can be useful when describing what is going on Changes the current working directory to the given path INFO lt output gt Writes output to the console Can be useful for debugging loops Example INFO Variable a is Sa Outputs the value of Sa CUDADEVICE lt id gt Sets the active CUDA device id see Section 6 5 for more details molegro virtual docker user manual 28 Appendix XI Script Commands page 227 251 IMPORT lt targets gt FROM lt file gt The IMPORT command reads molecular data from either PDB ENT Mol2 Mol SDF SD files lt targets gt is the usual syntax for specifying the molecules to import Notice Examples Files imported using the IMPORT command are always parsed using the currently set parser settings see PARSERSETTINGS command and prepared using the currently set preparation settings see PREPARE command Files are always appended to the workspace The workspace is not cleared You can clear the workspace using the NEW command
221. quests One agent must be installed on each computer on the virtual grid The agents receive job unit descriptions and spawn the Molegro Virtual Docker application Notice that Molegro Virtual Docker must be installed on the agent machine together with a valid license file Preparing a job for distributed execution can be done automatically by MVD for certain types of jobs A requirement is that the docking setup uses a DataSource for loading ligands see Chapter 5 A job unit is then created for each individual ligand in the DataSource This is a setup typical used for virtual screening MVD cannot automatically distribute all kinds of jobs such as docking a single ligand against multiple receptors but it is still possible to manually create a custom grid job file that can be distributed see Section 15 11 Molegro Virtual Docker is a single threaded program This means that when running MVD on a computer with multiple cores as nearly all modern CPUs features only a single core is used However Molegro Virtual Grid is able to run an instance of Molegro Virtual Docker for each core on the computer Therefore it may make sense to run Molegro Virtual Grid even if only a single computer is part of the grid No virtual grid license is necessary to run Molegro molegro virtual docker user manual 15 Molegro Virtual Grid page 180 251 Virtual Grid on a single machine Running Molegro Virtual Grid on multiple machines requires an extended
222. r Examples Dir C Test Molecules Pattern sdf mol2 Index 10 100 Dir C Test Pattern Stereo sdf Index 10 100 The Multifile data source takes a directory and scans it for the given pattern Patterns are specified using as a wildcard Notice that on Linux and Mac operating systems file patterns are case sensitive It is possible to specify more than one pattern by separating sub patterns with semi colons Patterns with semi colons must be surrounded by quotes As with file data sources it is possible to specify a subset using the molecule index specifier Index Notice that the Index specifier refers to the molecule index not the file index molegro virtual docker user manual 5 Data Sources page 83 251 5 2 Using Data Sources Data sources can be constructed and used in the following ways Specifying a Data Source in the Docking Wizard The first page in the Docking Wizard Choose Which Ligands To Dock allows you to choose to dock from a data source Notice that it is not possible to specify an RMSD reference ligand when docking with data sources since reference ligands must have compatible atoms and this cannot be checked for data sources The docking wizard creates a script where the DOCK command contains a reference to the specified data source see using data sources from a Script Choose Which Ligands to Dock From workspace M Ligands M BEN_1 A
223. r backward compatibility CO2minus Number of Carboxyl groups in ligand Csp2 Number of Sp2 hybridized carbon atoms in ligand Csp3 Number of Sp3 hybridized carbon atoms in ligand DOF Degrees of internal rotational freedom As of now this is the number of chosen rotatable bonds in the ligand and is thus equal to the Torsions term It is supposed to reflect how many rotational degrees of freedom are lost upon binding Future work may include a more advanced model where the actual conformation is molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 204 251 inspected in order to determine whether rotational degrees of freedom are lost N Number of nitrogen atoms in ligand Nplus Number of positively charged nitrogen atoms in ligand OH Number of hydroxyl groups in ligand OPO32minus Number of PO groups in ligand Os Number of ethers and thioethers in ligand carbonyl Number of Carbonyl groups in ligand halogen Number of Halogen groups in ligand Other terms RMSD The RMS deviation from a reference ligand if available molegro virtual docker user manual 19 Appendix Il PLANTS Scoring Function The PLANTS scoring function PLANTS Score used by MVD is derived from the PLANTS scoring function originally proposed by Korb et al KORB 2009 The MolDock scoring function further improves these scoring functions with a new hydrogen
224. r instance in order to reserve threads for other tasks It is not recommended to set the number higher than the number of physical CPU cores The log file for the agent can be retrieved using a web browser Open a browser and specify the IP number or DNS name of the agent on port 45454 e g http 192 168 1 101 45454 This will show the status and the log of the running agent It is also possible to obtain more verbose information by appending debug to the URL e g http 192 168 1 101 45454 debug Notice that the log file is also stored as a text file in the workingdir directory The web interface can be useful for obtaining information from an agent running without a GUI or to check if the communication between machines is being blocked by a firewall The controller loads a grid job description keeps track of the available resources the agents and distributes the individual job units to the agents It is also able to combine and filter the results collected from the agents Normally the grid controller is started directly from the docking wizard or Tools Virtual Grid Controller menu in MVD It is also possible to start the grid controller using the command line using the controller argument e g virtualgrid exe controller Optionally a grid job can be specified as well e g virtualgrid exe myjob gridjob controller If the controller is started from the docking wizard the automatically generated grid job
225. rarchical view of all macros The top level folders are mapped directly to corresponding menus in MVD That is View Rendering Preparation and Docking will appear as menus in the GUI It is possible to add new top level folder by selecting the root node RootFolder and pressing the New Folder button When a folder is highlighted in the Macro overview new macros can be added to it by pressing the New Macro button New or existing macros can be modified in the right pane Macro definition A macro consists of a Title which is the name that is shown in the corresponding menu an optional Label which can be used to assign an unique name to the macro so that it can be called from other macros this is done by using the macro invoke command i e macroname an optional Keyboard shortcut which is specified as text i e Alt F1 or Ctrl Shift 1 Shift A where the last shortcut simultaneously maps two alternative keyboard shortcuts and the actual Macro definition If macros or folders appear in red in the Macro overview it is because Hide from menu is enabled for them These items won t show up in the menus This can be useful for defining macros which will not show up in the GUI but still can be called from the Console Window It is also possible to add separators between the macros which will appear as menu separators in the GUI To add a separator between macros just use molegro virtual docker user manual 3 User Interfa
226. rd for each water displaced molegro virtual docker user manual 9 Displaceable Water page 142 251 Docking Wizard Choose Scoring Function and Define Binding Site Scoring function Score MolDock Score GRID Grid resolution A 0 30 Based on the current resolution and the search space size defined below the grid will require approx 89 7 MB of memory Ligand evaluation E Intemal ES 7 Intemal HBond Sp2 Sp2 Torsions V Displaceable Water Entropy reward for each water displaced 0 00 Binding site Origin User defined Center X 1 14 39 Z 16 78 Radius 15 P v Figure 91 Docking Wizard Enabling docking with Displaceable Water Since handling of displaced non displaced waters is done during the evaluation step only and therefore separated from the conformational search no other settings are needed to enable displaceable waters Scripting Settings It is also possible to enable displaceable water evaluation when performing batch job runs using the MVD scripting language The DisplaceWater true false option is used to toggle the displaceable water evaluation on or off and the entropy reward is specified using the DisplaceWaterReward 0 0 10 0 option Both settings are specified as parameters for the EVALUATOR command This is how a typical script using using displaceable water evaluation might look like DOCKSETTINGS maxIterations 1500 runs 10 ignoreSimilarPoses
227. rential evolution may use a cavity prediction algorithm introduced in Appendix IV Cavity Prediction to constrain predicted conformations poses during the search process More specifically if a candidate solution is positioned outside the cavity it is translated so that a randomly chosen ligand atom will be located within the region spanned by the cavity Naturally this strategy is only applied if a cavity has been found If no cavities are reported the search procedure does not constrain the candidate solutions One of the reasons why DE works so well is that the variation operator exploits the population diversity in the following manner Initially when the candidate solutions in the population are randomly generated the diversity is large Thus when offspring are created the differences between parental solutions are big resulting in large step sizes being used As the algorithm converges to better solutions the population diversity is lowered and the step sizes used to create offspring are lowered correspondingly Therefore by using the differences between other individuals in the population DE automatically adapts the step sizes used to create offspring as the search process converges toward good solutions molegro virtual docker user manual 20 Appendix III MolDock Optimizer page 209 251 Only ligand properties are represented in the individuals since the protein remains rigid during the docking simulation Thus a candida
228. reparation page 70 251 Notice The preparation options Always Never If Missing Remove applies to each individual molecule not each individual bond or atom For instance setting Assign bonds to If Missing results in covalent bonds being created for molecules not containing any bonds at all while molecules with bond information will preserve their bond assignments Likewise setting Create explicit hydrogens to If Missing will not add additional hydrogens to molecules containing e g polar hydrogens only In this case Always should be used if all hydrogens should be created This option allows to determine which atoms are connected covalently bound Two atoms are connected if their distance is more than 0 44 and less than the sum of their covalent radii plus a threshold of 0 45A the threshold is set to 0 4865A if one of the atoms is Phosphorus This options allows recognition of bond orders whether bonds are single double or triple the number of hydrogens attached to the atoms and their hybridization SP SP2 SP3 Also aromatic rings will be detected It should be noted that this assignment is not always perfect different protonation states can be difficult to assign properly A detailed description can be found in Appendix VII Automatic Preparation Notice The algorithm only assigns the number of implicit hydrogens to each atom No actual atoms will be added The next option Create explicit hydrogens al
229. ression The next section explains how to apply a model to docking results in the Pose Organizer The bottom panel Table columns determines which columns descriptors that are shown in the table on the first tab Table 1 describes the descriptors that are available New descriptors can be added from regression models created using Molegro Data Modeller see Chapter 13 for more details To add a new descriptor simply press the Add descriptor from regression model button and chose the regression model from a saved Molegro Data Modeling MDM file Notice that the regression model should only be using the same descriptors as the ones that are available in the DockingResults files only valid regression models will be available in the dialog The Pose Organiser shows a subset of the terms in the mvdresults file as columns in the Poses table Some of the terms use the same terminology as in the mvdresults file specifically Name Ligand Filename Workspace RerankScore Torsions RMSD MW LE1 LE3 Hbond Similarity Score Electro Hbond and Heavy Atoms but a few terms are renamed in order to better fit the column layout and for clarity molegro virtual docker user manual 7 Analyzing the Docking Results Column Name Description Name The internal name of the pose a concatenation of the pose id and ligand name Ligand The name of the ligand the pose was created from Workspace The workspace mvdml file co
230. ribution Doing this makes it possible to get a visual overview of the important parts of the ligand a Style Protein Atoms by Energy As above this scales the protein atoms according to their energy contributions Notice that protein atoms not interacting with the ligand are completely hidden To make all protein atoms visible again toggle the Hide Residues toolbar button molegro virtual docker user manual 7 Analyzing the Docking Results page 120 251 a Style Water Atoms by Energy This style makes it possible to get a visual overview of important interactions between water molecules and the ligand The radius of the water atoms is scaled proportionally to their energy contributions Water molecules with favorable interactions with the ligand are colored green and unfavorable interactions are colored red Water molecules with no interactions to the ligand are hidden If the Displaceable water evaluation option is selected the following coloring scheme applies see Chapter 9 for more details displaced waters are colored yellow non displaced waters are colored green if they are favorable and red if they are not favorable s Optimize Ligand and Protein Hydrogen Positions When docking with Molegro Virtual Docker the exact positions of the rotatable hydrogen atoms are not calculated Instead it is assumed that the hydrogens are pointing in the optimal direction In order to view the optimal direction of the rotatable hydrogens apply thi
231. rings for ligands cofactors poses and amino acids for proteins The atoms in a selection can be set to a custom color using the context menu invoked by pressing the right mouse button on a given atom Entire molecules can be set to a custom color using the Workspace Explorer molegro virtual docker user manual 3 User Interface page 39 251 context menu by selecting either Set Custom Color or Set Custom Color Carbons Only Custom Coloring is persistent it will persist after changing rendering coloring styles and takes precedence over any coloring style The Custom Coloring can be cleared using the Clear Custom Coloring option from the Workspace Explorer context menu or from the Visualization Window context menu when focusing on a given atom Notice that aromatic ring indicators pseudo bonds and single colored bonds will only have custom coloring applied if the entire molecule is selected or if the Set Custom Color command is invoked from the Workspace Explorer context menu The Custom Coloring information is stored together with the atoms in MVDML files and will be used every time the MVDML workspace file is opened in MVD 5 L0 LCIedatink Lave iS To create labels use the Create Label dialog which can be invoked via Create Labels in the Workspace Explorer context menu on molecular categories Proteins Ligands and Poses or via the Tools Labels menus Create Label Label Type Atom Template
232. roblems running the software on your system a Mac OS X 10 6 Intel and later versions If you discover a program error please mail the information to support clcbio com Remember to specify how the error can be reproduced the version number of Molegro Virtual Docker in question and the operating system that was used If possible inclusion of molecular files used e g Mol2 PDB MVDML will make it easier for us to reproduce and correct the error molegro virtual docker user manual 1 Introduction to Molegro Virtual Docker page 9 251 The following formatting styles are used in this manual a All GUI text labels and keyboard shortcuts are written in bold face with initial capital letters Examples Workspace Explorer Macro Definition Ctrl O Menus and menu items are identified using dividing lines and bold face Example View Docking View indicates that the user should first select the View menu and then select the Docking View menu item a Filenames are written in mono spaced font Example Molegro MVD bin mvd exe The keyboard shortcuts used in the manual works for Windows and Linux versions of MVD On Mac OS X the CTRL key is replaced by the command key and function key shortcuts e g F1 should be invoked by pressing the function key and the fn key e g fn F1 The screenshots used in the manual are taken from the Windows XP and Vista versions of MVD Therefore dialogs and other GUI related mater
233. roperties Window If three connected atoms are selected the angle that they span will be shown in the Properties Window If no atoms are selected and a bond is highlighted the field Torsion Angles in the Properties Window will show the torsion angle s defined through this bond molegro virtual docker user manual 3 User Interface page 38 251 Point Annotation 7 Distance 2 47 A Torsion 4 19 a R Angle 26 89 Selection Deselect All Set Selection as Center of Search Space Set Selection as Center of Distance Constraint Create Distance Annotation Nitrogen Atom Set as Center of Search Space Create Distance Constraint Set as Rotational Center Figure 28 Annotations and measurements Measurements can also be made permanent as annotations There are different kinds of annotations To create annotations select 1 4 atoms and use the context menu right click mouse button and choose Create Annotation The text can be edited before the annotation label is created Annotations are added to the Workspace Explorer category Annotations Annotations can also be removed from the workspace using the context menu available from the Annotations category in the Workspace Explorer window Atoms can be manually selected in the Visualization Window using the mouse Using the context menu when focusing on a specific atom it is also possible to select deselect atoms molecules molecules carbon only
234. rtcut for invoking this dialog the functionality is the same as described in Section 3 9 The text window at the bottom displays information about the currently selected residue Here it is possible to see the different protonation states and any errors may be inspected here molegro virtual docker user manual 4 Preparation page 75 251 Atom GLU GLZ GLZ1 E CA CB cD CG N 8 OE1 0h 0 5e Oh h OE2 0h 0 5e h Oh Figure 56 Example of protonation state Some fields for the alternative protonations GLZ and GLZ1 are blank These blank fields must match the base protonation GLU in order for a residue to match an alternative protonation All protonation states consist of a base or default protonation which describes the number of hydrogens for each atom the bonding between atoms and their charge The base protonation is listed as the first column in the table in figure the base protonation is listed in the GLU column Alternative protonations are modifications to this base scheme In Figure 56 the GLZ and GLZ1 columns are modifications to the GLU scheme they provide only information for some of the atoms in the residue in this case OE1 and OE2 For a residue to match an alternative protonation the atoms must match the properties described by the alternative protonation while any atom not described by the alternative protonation must match the base protonation Finally the protonation tab also provides t
235. s items Options v Workspace New Backbones 1 O Cavities 1 H Constraints 1 Interactions 11 Ligands 1 Active BTN_300 Proteins 1 O Surfaces 1 O Water 84 Value Single 1326 1 09 435 1304 Dihedral angles f Figure 21 Main window showing different visualization styles The easiest way to get acquainted with the different drawing modes is to try the preset modes listed in the Rendering menu or to use the Visualization Settings dialog to inspect and modify visualization settings described in Section 3 22 Afterwards use the Macro and Menu Editor described in Section 3 27 to explore which console commands that are used for a particular view 3 User Interface page 31 251 Navigating the 3D World Mouse actions available in the 3D world Function Action Zoom By pressing both mouse buttons and moving up and down By using scroll wheel By using shift and left mouse button Free Rotation Dragging mouse cursor while holding left mouse button down Drag Atom Rotation While holding mouse over an atom Dragging mouse left mouse button down will force the atom to follow the mouse cursor Free Translation Dragging mouse cursor while holding right mouse button down Show Context Menu Click and release right mouse button All rotations are centered about the rotational center This center can be chosen by invoking the context menu on an atom right mouse button
236. s bond connects The order attribute describes the bond order 1 single bond 2 double bond and 1 5 delocalized bond lt Protonation gt name refers to the name that will be used as display name and identifier in the GUI pdbAlias and description are purely informational molegro virtual docker user manual 5 Data Sources There are several ways to import ligands and prepare them for docking in Molegro Virtual Docker Ligands can be imported in the GUI using Import Molecules from the File menu and included in the workspace before docking This is the easiest way to import data but it can be slow if working with thousands of ligands Ligands can be imported using the IMPORT script commands This has the disadvantage that all of the input file is parsed e g a SDF file containing 2000 entries will have to be completely loaded and prepared in memory even if only a subset of it is needed It is also necessary to modify the MVD scripts manually Ligands can be read from a Data Source Ligands are streamed from a source such as a large file and only one molecule is loaded into memory at a time Currently two types of data sources are available in Molegro Virtual Docker File data sources These are single files containing multiple structures such as SDF multi molecule Mol2 or MVDML It is possible to read a subset of the molecules contained in the file Multifile
237. s can be tested by pressing Test Macro before they are stored permanently It is possible to edit existing views in the Macro and molegro virtual docker user manual 3 User Interface page 56 251 Menu Editor The default visualization settings used by MVD can be changed by pressing the Use as Default Settings button If needed the default visualization settings can also be restored to the factory settings by pressing the Restore Default Settings to Factory Settings button The factory settings are the initial settings used by MVD when started for the first time At that point the factory settings are also used as the default visualization settings The current visualization settings shown in the Visualization Settings dialog will be stored in the MVDML workspace file when saving the workspace When importing workspaces containing visualization settings these stored settings will be used instead of the default settings Notice When making a new workspace or clearing the current workspace the default visualization settings will be used It is possible to create high quality screenshots by selecting Rendering High Quality Render Raytrace The High Quality Render Raytrace dialog makes is possible to create images in arbitrary size and higher quality than when saving screenshots from the OpenGL view The High quality render uses a raytrace engine to create the output image This has some graphical advantages as compared to the
238. s file uses a deliberately simple charge scheme where only a few atoms are assigned charge see Appendix I MolDock Scoring Function If however the receptor has been prepared in another program with another charge assignment scheme and saved in a format such as Mol2 which supports partial atomic charges uncheck this option in order not to receive several of warnings about wrong atomic partial charge Notice that this setting affects both the validation and how protonation states are changed When a protonation state is changed from the protein preparation dialog the charges are only modified if this setting is checked Check and correct non polar atoms carbons Some PDB files contain only explicit hydrogen information for the polar atoms Since the hydrogen information for non polar atoms the carbons is not used by the MolDock score during the docking it is not necessary to have them explicitly attached Therefore by default only the hydrogen count for polar atoms is checked As above this setting affects both the validation and how protonation states are changed When a protonation state is changed from the protein preparation dialog hydrogens on non polar atoms are only modified if this setting is checked V Check and correct charges Check and corect non polar atoms carbons Minimization Settings Maximum steps per residue 1000 Maximum global steps 1000 Residue neighbour distance A 0 00 Choose molecules to
239. s often referred to as the parent and the resulting solution after modification is called the offspring Sometimes more than one parent is used to create the offspring by recombination of solutions which is also referred to as crossover Figure 122 below shows an outline of the evolutionary process taking place in EAs The guided differential evolution algorithm MolDock Optimizer used in MVD is based on an EA variant called differential evolution DE The DE algorithm was introduced by Storn and Price in 1995 STORN 1995 Compared to more widely known EA based techniques e g genetic algorithms evolutionary programming and evolution strategies DE uses a different approach to select and modify candidate solutions individuals The main innovative idea in DE is to create offspring from a weighted difference of parent solutions The DE works as follows First all individuals are initialized and evaluated according to the docking scoring function fitness function used Afterwards the following process will be executed as long as the termination condition is not fulfilled For each individual in the population an offspring is created by adding a weighted difference of the parent solutions which are randomly selected from the population Afterwards the offspring replaces the parent if and only if it is more fit Otherwise the parent survives and is passed on to the next generation iteration of the algorithm Additionally guided diffe
240. s option Any rotatable hydrogens on the protein and ligand which are involved in hydrogen bonds will be oriented to the optimal direction a Minimize Ligand This performs an energy minimization of the current molecule with regard to its MolDock score energy Figure 80 An example of the Style Ligand Atoms by Energy visualization where atoms are scaled according to their energy contributions The Ligand tab page consists of three tables The Atom Energies table shows information about individual atoms in the ligand When hovering the mouse over an atom in the 3D view it will molegro virtual docker user manual 7 Analyzing the Docking Results page 121 251 automatically be highlighted in the table Similarly when selecting entries in the table atoms will be selected in the 3D GUI It is possible to show or hide this table using the Options drop down menu The following types of energy contributions may be listed for a ligand atom a EPair This is the pairwise PLP steric and hydrogen bonding energy between a ligand atom and a receptor atom Pairwise interactions between a ligand and either cofactors or water molecules will show up as EPair cofactor and EPair water a EIntra This is the internal ligand energy between a ligand atom and the other atoms in the ligand a EElec This is the pairwise electrostatic interactions For the protein they are divided into long range and short range interactions EEl
241. s that the proteins water molecules and cofactors currently in the workspace are taken into account If the workspace has been changed the energy displayed here may not be the same as the one displayed in the Pose Organizer since these were assigned during the docking evaluation molegro virtual docker user manual 7 Analyzing the Docking Results 5 _Ligand E nergy nspector ligand pose XK2_263 Hide other ligands poses Targets Total Energy Settings ID Name Total 0 6 42352 1 O 9 92978 2 N 2 80002 3 C 5 57079 AAD EPair EPair cofactor Elntra 4 76673 0 10 5101 0 2 27183 0 4 35638 0 A Hydrogen Bonds and Strong Bectrostatic interactions ID Donor Energy target ligand Length 3 16611 3 0145 2 86465 3 23719 A AAO Allatoms 46 Total Elntra 230 32 0 476109 Copy tables to clipboard Figure 79 The Ligand Energy Inspector page 119 251 Using the Ligand pose combo box it is possible to browse through the ligands and poses available in the Workspace To avoid visualization of other ligands and poses when inspecting a molecule you can toggle on the Hide other ligands poses check box Besides inspecting the various energy contributions it is possible to perform various actions using the Action drop down menu a Style Ligand Atoms by Energy This will scale the radius of the ligand atoms proportionally to their energy cont
242. se are two chains from the same protein It also indicates that a ligand has been detected in the PDB file Choosing Preparation Types Select the Preparation tab see Figure 3 Some structures contain information about bond types and bond orders and have explicit hydrogens assigned However PDB files often have poor or missing assignment of explicit hydrogens and the PDB file format cannot accommodate bond order information Set Assign All Below to Always This ensures that all preparation will be done by MVD molegro virtual docker user manual 2 Docking Tutorial page 13 251 Custom If Missing If Missing Create explicit hydrogens f Missing Assign charges calculated by MVD Always Detect flexible torsions in ligands Always Assign Tripos atom types ff Missing Notice The preparation options If Missing Always Never Remove applies to each individual molecule not each individual bond or atom For instance setting Assign bonds to If Missing results in covalent bonds being created for molecules not containing any bonds at all while molecules with bond information will preserve their bond assignments Likewise setting Create explicit hydrogens to f Missing will not add additional hydrogens to molecules containing e g polar hydrogens only In this case Always should be used if all hydrogens should be created Figure 3 Preparing the PDB file If the protein structure h
243. se of the stochastic nature of the docking engine more than one docking run may be needed to identify the correct binding mode The docking run can also be stopped by pressing the Stop batchjob button When the docking run finishes the poses found are saved to the Output directory specified previously in the Docking Wizard dialog here c Program Files Molegro MVD ScriptOutput was used The poses found can now be imported into MVD by 1 Selecting Import Docking Results mvdresults from the File menu using the DockingResults mvdresults file molegro virtual docker user manual 2 Docking Tutorial page 21 251 2 Dragging and dropping the DockingResults mvdresults file onto the MVD application 3 Dragging and dropping the DockingResults icon Eri onto the MVD application The DockingResults mvdresults file is located in the Output directory together with a docking log file and the poses found in Mol2 file format After importing the DockingResults mvdresults file the Pose Organizer will appear showing the poses found see Figure 13 1 13816 3 03842 Dynamic update notice disables multiple poses selection E Only show top 1 poses for each ligand Open checked poses in Data Analyzer Sorting criteria 1st Ligand 2nd MolDock Score 3rd None Pressing OK will keep 1 and ignore 3 poses Figure 13 The predicted poses The Pose Organ
244. se section the basic license makes it possible to run jobs on only one agent at a time If an extended license has been obtained install it by going to the Help menu and choose Install license and specify the location of a valid Molegro Virtual Grid license file Notice that is possible to see information about the current license by choosing Help About Molegro Virtual Grid Viivesral fyi Virtual Grid The Docking Wizard in MVD makes it possible to create MVG jobs automatically when docking a DataSource with multiple ligands against a single protein molegro virtual docker user manual 15 Molegro Virtual Grid page 189 251 target Other cases such as docking a number of ligands against different receptors require manual creation of MVG job file A MVG job is an XML file that describes a number of job units The typical format is lt Job id 63647969 d2c5 496a 944a 3edcbac43d8c description Job gt lt Before uploadFiles Unnamed_complex mvdml gt DOCKSETTINGS maxIterations 1500 runs 10 EVALUATORTYPE MolDockGrid EVALUATOR cropdistance 0 gridresolution 0 30 OPTIMIZERTYPE MSE OPTIMIZER populationsize 50 cavity true LOAD Unnamed complex mvdml lt Before gt lt Unit id 0 uploadFiles ZINC02000919 mvdml gt Dock File ZINC02000919 mvdml lt Unit gt lt Unit id 1 uploadFiles ZINC03775575 mvdml gt Dock File Z1INC03775575 mvdml lt Unit gt lt Unit id 2 uploadFiles ZINC00006989 mvdml
245. tab it is possible to customize the similarity score It is possible to enable or disable different template groups and to adjust the Gaussian function used to compare the atom overlap with the group centers The following groups can be chosen a Steric The steric group matches all atoms It is used for shape matching without taking any chemical groups into account a Hydrogen Donor Matches any hydrogen donor atom Hydrogen Acceptor Matches any hydrogen acceptor atom Negative Charge Matches negatively charged atoms Notice that atoms with a numerical charge less than the specified Charge threshold are not considered charged molegro virtual docker user manual 10 Template Docking page 152 251 a Positive Charge Similar to negative charge as described above but for positively charged atoms a Ring Matches all atoms which are part of rings both aromatic and aliphatic The list view shows the following information a Radius The characteristic radius ro for the template group see Template Scoring Function above a Strength The strength w or weight for the template group a Count The number of centers in the group The different template groups will be visualized in the visualization window with a sphere for each center in the template group Different template groups will be colored in different colors The small graph in the lower left corner shows the strength of the potential for the selected gro
246. take into account Cofactors 1 1 F Water 62 62 F Proteins 1 1 z Ligands 1 1 Choose Visible Figure 58 The Settings tab molegro virtual docker user manual 4 Preparation page 78 251 Minimization Settings The minimization options are the same as the ones described in the Sidechain Minimization section see 3 20 The only difference is the inclusion of the Residue neighbour distance A which determines how close residues must be in order to be considered neighbours this criteria is described in the The Mutate and Optimize Tab section The protonation templates are defined in the misc data residues xml file It is possible to manually modify and extend this file with new protonation patterns but we strongly advise that a backup copy of the original file is made before doing so The protonation template file must be valid XML Wikipedia offers an introduction to XML at http en wikipedia org wiki Xml The overall structure of the XML file is illustrated with the following fragment from the protonation template file lt ResidueDefinitions gt lt Residue name ASP letter D longName Aspartate pdbAlias ASP gt lt Atom pdbName C hyb 2 charge 0 hydrogens 0 element C gt lt Atom pdbName CA hyb 3 charge 0 hydrogens 1 element C gt lt Atom pdbName CB hyb 3 charge 0 hydrogens 2 element C gt lt Atom pdbName CG hyb 2 charg
247. te solution is encoded by an array of real valued numbers representing ligand position orientation and conformation as Cartesian coordinates for the ligand translation four variables specifying the ligand orientation encoded as a rotation vector and a rotation angle and one angle for each flexible torsion angle in the ligand if any Each individual in the initial population is assigned a random position within the search space region defined by the user Initializing the orientation is more complicated By just choosing uniform random numbers for the orientation axis between 1 0 and 1 0 followed by normalization of the values to form a unit vector and the angle of rotation between 180 and 1802 the initial population would be biased towards the identity orientation i e no rotation To avoid this bias the algorithm by Shoemake et al GSHOEMAKE 1992 for generating uniform random quaternions is used and the random quaternions are then converted to their rotation axis rotation angle representation The flexible torsion angles if any are assigned a random angle between 180 and 180 In MVD the following default parameters are used for the guided differential evolution algorithm population size 50 crossover rate 0 9 and scaling factor 0 5 These settings have been found by trial and error and are generally found to give the best results across a test set of 77 complexes molegro virtual docker user manu
248. ted Removes all sidechains that are not highlighted in the sidechain list Sidechains added to the list will be visualized with a wireframe sphere in the 3D Visualization window If one or more sidechains are highlighted in the list only this subset will be visualized The list of chosen sidechains contains the following information Residue The residue name id Protein ID The protein or protein chain ID and name Tolerance See below Strength See below Flexible Indicates whether the sidechain is currently selected for minimization in the docking simulation or not By default all sidechains added to the list will be set as flexible however it is possible to add sidechains to the list and only have their potential softened while keeping them rigid Torsions The number of degrees of freedom in the given sidechain The degrees of freedom that are minimized during the docking simulation are the torsional angles in the sidechain Mean T The temperature factor or B factor is a measure of how much a given atom vibrates around its position in the crystallographic model This can be useful since a high B factor may indicate that the residue is flexible Mean T is the average temperature for the heavy atoms in the sidechain Max T The same as above except that Max T is the single highest temperature factor of all heavy atoms in the sidechain molegro virtual docker user manual 8 Sidechain Flexibility page 134 25
249. teins 4 17A Covalent radius 0 68 A Hydrogen bo Nonpolar Pattial charge 0 Hybridization Sp3 Show L E Inspector Redo Layout 13 21 36 201 __ Evaluating molecule XK2_263 A Figure 84 The Ligand Map window At the top of the Ligand Map window it is possible to choose between the currently shown molecule and whether to hide other ligands and poses It is possible to select atoms synchronously in the 2D and 3D window by clicking on them It is also possible to invoke the standard context menu by right clicking on an atom This makes it possible to e g change atom properties or create constraints By clicking on the Show Interactions map the interactions between the current ligand pose and the receptor is shown These interactions are the ones reported by the Ligand Energy Inspector It is possible to press the Show L E Inspector button which will open the Ligand Energy Inspector and make it possible to adjust the scoring function settings or change the scoring function By default only hydrogen bond interactions are shown It is possible to show electrostatic interactions and steric interactions as well by checking the respective checkboxes It is also possible to set a minimum interaction threshold for each type of interaction Raising the threshold slider limits the number of interactions shown The specific value of the minimum interaction molegro virtual docker user manual 7 Analyzing the D
250. the binding site Thus atoms more than Radius angstroms away from the center of the binding site are ignored in the scoring function This reduces the overall computing time significantly when working on large molecules Notice that charged atoms capable of long range interactions are always taken into account in the scoring function The Enforce hydrogen bond directionality option is used to check if bonding between potential hydrogen bond donors and acceptors can occur If hydrogen bonding is possible the hydrogen bond energy contribution to the docking score is assigned a penalty based on the deviations from the ideal bonding angle Using this option can significantly reduce the number of unlikely hydrogen bonds reported molegro virtual docker user manual 6 Docking Functionality page 93 251 The Ligand evaluation can also be customized Internal ES toggles whether internal electrostatic interactions should be calculated for a pose Internal Hbond toggles whether a pose should be allowed to have internal hydrogen bonds and Sp2 Sp2 Torsions determines whether an additional dihedral term should be added for taking Sp2 Sp2 bonds into account see Appendix I MolDock Scoring Function Scoring function Score MolDock Score GRID Grid resolution A 0 30 Based on the current resolution and the search space size defined below the grid will require approx 89 7 MB of memory Ligand evaluation E Intemal ES F Intemal HBond
251. the Add agents manually button It is possible to enter a list with IP numbers or DNS names of computers to be added or to load a list from a text file When an agent appears on the list the following actions are available using the context menu Show status Display statistics about the currently running jobs Reset agent This terminates all running jobs on the agent and removes all temporary files produced Notice that this will also cancel all jobs and delete all files belonging to another user Resetting the agent can be useful in order to cancel jobs on the agent or to clean up temporary files molegro virtual docker user manual 15 Molegro Virtual Grid page 187 251 Remove from list Removes the agent useful for instance if the agent belongs to or is used by another user on the same network If Auto discover is enabled the agent might re appear Notice that the Agents menu contains an option for removing all non responding agents The Agent menu offers a few additional options for setting the process priority normally agents execute job units with a process priority just below the normal priority It is possible to adjust the priority to either normal which is the typical priority user processes on an OS is assigned or to idle which means the job will only execute if no other process requests CPU time Notice that the controller process priority may be overruled by the agent priority command lin
252. the Workspace Explorer window Figure 39 molegro virtual docker user manual 3 User Interface page 49 251 SENN T TORE Workspace Explorer x tems Options Workspace Unnamed Flexible Residues 44 Ligands 1 Poses 2 Proteins 1 Original conformation v Edit Original conformation Minimized to Energy 634 28 08 STR_1 conformation 10 STR_1 conformation Figure 39 Receptor conformation list In order to manipulate receptor conformations select the appropriate conformation and press the Edit drop down button in the lower right corner of the Workspace Explorer Figure 40 items Options 7 Workspace Unnamed Flexible Residues 44 Ligands 1 Poses 2 H Proteins 1 K K i K K T08 STR_1 confomation Edit Di Property Value Clone to new protein s Set as new default conformation Figure 40 Actions for receptor conformations You can delete a conformation Delete or choose Clone to new protein s to clone the current conformation to one or more new proteins if the conformation consists of torsional changes to more than one protein or molegro virtual docker user manual 3 User Interface page 50 251 protein chain a clone will be made for each protein The last option Set as new default conformation will make the currently selected conformation the only conformation in the workspace all other conformations will b
253. the pose is energy minimized It is possible to define the maximum number of global and local minimization steps The receptor and ligand minimization is performed using the Nelder Mead simplex algorithm and is described in more detail in Section 3 20 Notice that is advisable to use Tabu Clustering during the docking simulation in order to ensure a greater diversity of the returned poses See the Docking Wizard Section 6 3 for more information 8 3 Sidechain Flexibility and Scripting If using sidechain flexibility together with scripting first add a sidechain flexibility description to the workspace The actual softening of the potentials and post docking minimization steps can be scripted using the molegro virtual docker user manual 8 Sidechain Flexibility page 138 251 MinimizeReceptor LocalSteps GlobalSteps option for the DockSettings command and the SoftenPotential true false option for the evaluator Notice that it is advisable to use Tabu Clustering to ensure greater diversity of the returned poses before the minimization run is executed This is how a typical script using sidechain flexibility might look like DOCKSETTINGS maxIterations 2000 runs 20 ignoreSimilarPoses false IgnoreSimilarPosesThreshold 1 MaxPoses 5 MinimizeReceptor 2000 2000 EVALUATORTYPE MolDockGrid EVALUATOR cropdistance 0 gridresolution 0 30 hbond90 true SoftenPotential true tabuclustering true 2 100 id
254. the red graph shows the mean energy of the entire population of candidate solutions see Appendix III MolDock Optimizer for more details about the docking simulation and the population terminology Notice The red graph is only shown when using the MolDock Optimizer docking algorithm molegro virtual docker user manual page 103 251 6 Docking Functionality page 104 251 Batchjob Running Batchjob started ma 27 aug 10 12 41 2012 Bapsed 00 00 16 Finish estimated 10 13 21 Remaining 00 00 23 Working path C Users Mikael Documents MVD Data DockingOutput 227 Current ligand 5 10 rus pms Log Poses curent igand 13 Poses all Graph Curent script 0 20 40 60 Blue Energy of best pose Red Mean Energy of candidate population Status Docking BEN_1 AJ from Unnamed_complex mvdml Figure 73 Docking progress dialog with convergence graph shown 6 4 Run Docking in Multiple Processes The default docking option Run docking in separate process is single threaded which means only a single CPU core is utilized By running the docking simulation in multiple processes it is possible to take advantage of the multiple cores present in modern CPU s or multi processor systems In most cases the optimal number of processes correspond to the number of physical not virtual cores in the system Notice that there may also be a speed advantage to using multiple CPU thre
255. tion and setting the Number of runs to 50 The Parameter Settings show the parameters used by the MolDock Optimizer search algorithm The default values shown are generally suitable for most docking tasks See Appendix III MolDock Optimizer for details on MolDock Optimizer parameter settings The MolDock SE and Iterated Simplex algorithms and their parameters are further described in Appendix XII MolDock SE and Appendix XIII Iterated Simplex molegro virtual docker user manual 6 Docking Functionality page 97 251 Customize Search Algorithm Search algorithm Algorithm MolDock Optimizer Number of runs 10 V Constrain poses to cavity After docking Energy Minimization V Optimize H Bonds Parameter settings Population size Max iterations Scaling factor 0 50 Crossover rate 0 90 Offspring scheme Scheme 1 Temination scheme Variance based Figure 68 Customizing the search algorithm Instead of returning only one final pose for each docking run it is possible to return multiple poses representing different potential binding modes This can be useful when the best scoring i e lowest energy pose does not represent the native binding mode or when multiple binding modes exists Here clustering can be used to reduce the number of poses found during the docking run and only the most promising ones will be reported If multiple poses are returned for each run the following options are availabl
256. tion energy 9 4 j E prp r se ij E inter i ligand j protein The summation runs over all heavy atoms in the ligand and all heavy atoms in the protein including any cofactor atoms and water molecule atoms that might be present The Epp term is a piecewise linear potential described below The second term describes the electrostatic interactions between charged atoms It is a Coulomb potential with a distance dependent dielectric constant given by D r 4r The numerical value of 332 0 fixes the units of the electrostatic energy to kilocalories per mole To ensure that no energy contribution can be higher than the clash penalty the electrostatic energy is cut off at the level corresponding to a distance of 2 0 for distances less than 2 0 Notice that although the electrostatic energy contribution has the theoretically predicted molegro virtual docker user manual 18 Appendix I MolDock Scoring Function page 199 251 magnitude the other energy terms are empirically motivated and the total energy does not necessarily correlate with the true binding affinity The charges are set according to the scheme listed in Table 3 Metal ions are assigned a charge of 1 e g Na or 2 e g Zn Ca Fe charge ligand atoms protein atoms 0 5 N atoms in C NH2 2 His ND1 NE2 Arg NH1 NH2 1 0 N atoms in N CHs3 2 Lys N NH3 0 5 O atoms in COO SO4 Asp OD1 0D2 PO2 PO2 Glu OE1 0E2 0 66 O atoms in P
257. tor 2 0 RotVector 3 0 RotAngle 0 Reset All to Defaults Figure 85 Pose Modifier dialog Notice It is not possible to directly modify poses after the workspace has been molegro virtual docker user manual 7 Analyzing the Docking Results page 130 251 saved and reloaded However ligands can be modified any time To modify poses saved these can be converted to ligands and modified afterwards which will result in a new modified pose Different interactions can also be visualized on the fly Dynamic Update tab The RMSD Matrix dialog can be used to quickly inspect deviations between molecules in the workspace In addition to the standard measure Pairwise Atom Atom RMSD by ID two variants Pairwise Atom Atom RMSD checking all automorphisms and Pairwise Atom Atom RMSD by nearest unmatched neighbour of the RMSD measure tries to take intrinsic symmetries of the molecule into account when calculating RMSD The recommended choice is Pairwise Atom Atom RMSD checking all automorphisms which is also used by default Pairwise Atom Atom RMSD checking all automorphisms Name 0 i 0 XK2_263 1 Copy of XK2_263 0 2 XK2_263 0 9 0 9 3 00 XK2_263 0 524027 0 524027 4 01 XK2_263 1 30083 1 30083 5 02 XK2_263 1 13816 1 13816 4 Molecule 1 Figure 86 RMSD Matrix dialog The dialog can be invoked by choosing RMSD Matrix from the Tools menu The Copy to Clipboard button can be used
258. true MaxPoses 5 IgnoreSimilarPosesThreshold 1 molegro virtual docker user manual 9 Displaceable Water page 143 251 EVALUATORTYPE MolDockGrid EVALUATOR cropdistance 0 gridresolution 0 30 ligandes false sp2sp2bond false internalhbond false hbond90 true DisplaceWater true DisplaceWaterReward 0 OPTIMIZERTYPE MSE OPTIMIZER populationsize 50 cavity true creationEnergyThreshold 100 poseGenerator 10 10 30 recombine true maxsimplex 750 simplexsteps 300 simplexd istancefactor 1 clusterthreshold 1 00 keepmaxposes 5 LOAD SomeComplex mvdml DOCK After docking using the displaceable water evaluation it is possible to inspect the docking results in the Pose Organizer or in the Ligand Energy Inspector When inspecting the docking results in the Pose Organizer it is possible to see the overall energy contributions summarizing interactions between non displaced waters and the ligand combined with energy contributions and entropy rewards for displaced water molecules These contributions are listed in the DisplacedWater column which can be enabled from the list of optional columns Using the Ligand Energy Inspector introduced in Section 7 3 it is possible to inspect the displaceable water evaluation in more details In short the Ligand Energy Inspector dialog allows for easy inspection of displaced non displaced waters energy contributions from displaced non disp
259. ty Mouse preferences on Mac OS X The final settings tab Parsing contains the Minimum protein size PDB import option This option is used for setting the minimum number of heavy atoms required for parsing a molecule as a protein during PDB import default is 69 heavy atoms If the parsed molecule contains less heavy atoms than the specified threshold value it is parsed as a ligand and residue information is ignored The Parsing tab also determines how MVD handles non standard characters such as special national characters This setting is used when importing and exporting molecular structures in text file format such as SDF Mol2 PDB files and when working with other text files such as mvdresults and mvdscript XML files Such as MVDs internal MVDML file format are always stored as UTF 8 Notice that the Batch Job Script Parser always uses UTF 8 as default encoding it runs in another process and is not aware of the MVD settings molegro virtual docker user manual 11 Customizing Molegro Virtual Docker page 162 251 General Graphics Mouse Minimum protein size PDB Mol2 import 69 fa Default File Encoding UTF 8 also reads UTF 16 and ASCII Break unrealistic bonds during import Mol2 SDF V Combine Mol2 substructures and small PDB molecules with same chain ID 7 Use hybridization from Sybyl atom types SDF data header for molecule names SDF files only Reset All
260. ude hydrogens in torsion term toggles whether or not hydrogens should be included when calculating the Tripos torsion potential ftors To use the PLANTS scoring function the EVALUATORTYPE script command has to be set Moreover specific scoring function parameters are set by the EVALUATOR script command see Appendix XI Script Commands for more details molegro virtual docker user manual 20 Appendix Ill MolDock Optimizer The MolDock Optimizer search algorithm MolDock Optimizer used in MVD is based on an evolutionary algorithm MICHALEWICZ 1992 2000 Evolutionary algorithms EAs are iterative optimization techniques inspired by Darwinian evolution theory In EAs the evolutionary process is simplified and thus it has very little in common with real world evolution Nevertheless during the last fifty years EAs have proved their worth as powerful optimization techniques that can assist or replace traditional techniques when these fail or are inadequate for the task to be solved Initialization Fitness Population Evaluation Selection A S ti Recombination Figure 122 Outline of evolutionary algorithm molegro virtual docker user manual 20 Appendix III MolDock Optimizer page 208 251 Basically an EA consists of a population of individuals candidate solutions which is exposed to random variation by means of variation operators such as mutation and recombination The individual being altered i
261. ues are normalized so a value of 1 0 corresponds to an optimal match Each row in the spreadsheet corresponds to a ligand or pose and each column corresponds to the overlap with a template group center The columns are named Sx for the steric group centers HDx for hydrogen donors centers HAx for hydrogen acceptors and Posx Negx and Ringx for the positive negative and ring atom groups where x is an index Each group also has a sub total match designated by an ALL suffix e g HD ALL FU Molegro Data Modelleg File Edit Preparation Modelling Visualization Window Modules Help ena S il E amp IE T amp Selection Descriptors A Coloring Defaut f Search E Name HDO HD ALL HAO HAI HA2 HA3 HA4 HAS HAG HA ALL NegO 1 iteh 0 363355 0 363355 0 831156 0 94982 0 779316 0 906162 0 00223798 0 360908 0 00150405 0 576631 0 779319 2 tsg_kplh 0 542797 0 542797 1 03265 0 805367 0 524483 0 723581 0 0266389 0 539142 6 75803e 05 0 554455 0 524468 3 tsh _kolh 1 1 1 1 1 1 1 1 1 1 1 4 Isi_kpLh 0 471996 0 471996 1 05698 0 836454 0 733299 0 694617 0 00291613 0 468818 0 00430302 0 57605 0 733282 5 Isi_kplh 0 0591898 0 0591898 0 965159 0 603711 0 525257 0 7983 0 0496297 0 0587913 1 04383e 06 0 45892 0 525208 tems 5 Workspace Unnamed S Datasets 1 te Terms Time Description 15 10 05 396 MOM build MDM 2073 3 0 0 Released e 15 10 05 396 Th
262. und In order for MVD to be able to perform optimally the molecules in the workspace must be properly prepared before the docking begins The molecules can either be prepared internally in MVD or externally by another program e g MOE from CCG CCG or Maestro from Schr dinger LLC SCHRODINGER In this tutorial we will use the built in preparation method available in MVD If the workspace is not empty start by clearing it select File Clear Workspace Next we will add some structures This can be accomplished by selecting File Import Molecules or by dragging and dropping a molecule structure file MVD supports PDB Mol2 SDF and its own XML based format MVDML Start by importing the file 1HVR pdb from the installation examples directory located in the MVD installation folder This file a HIV 1 protease complexed with XK263 is an unmodified file taken from the RCSB Protein Data Bank www pdb org molegro virtual docker user manual 2 Docking Tutorial page 12 251 Choosing Molecules to Import The Import Molecules dialog see Figure 2 appears Select which molecules to import Water 150 150 Proteins 1 1 5 Import small molecules as Ligands Replace or add to workspace Add to current workspace x Figure 2 Importing 1HVR from the PDB file Deselect the cofactors since we will not need these for this example The import dialog shows two proteins actually the
263. unds similar to one or more reference molecules for instance the reference molecules could be compounds known to bind strongly to a target receptor under investigation It is easy to search for similar compounds in the Molegro Data Modeller using the built in Similarity Browser described in Section 13 Mc If a quantitative measure is known for instance the experimental binding affinity these values may be added as a column in Molegro Data Modeller It molegro virtual docker user manual 14 Molecular Descriptor Calculations page 175 251 is then possible to create a regression model where the molecular descriptors are used as the independent variables and the measured quantity as the target variable Molegro Data Modeller provides several techniques for building regression models including Multiple Linear Regression Partial Least Squares Support Vector Machines and dimensionality reduction techniques Molegro Data Modeller also offers advanced methods for clustering including k nearest neighbours and a density based clustering scheme and classification and methods for detecting outliers and creating diverse subsets The CFDM descriptor is an unique set of descriptors created by Molegro with the following properties a Independence of the conformation of the molecule They are based on the topological properties of the molecule a A small set of descriptors Having a small number of descriptors makes it easier to
264. up as a function of radial distance The vertical blue line indicates the characteristic radius ro Adjust the parameters as needed and press OK to add the template to the workspace a strepta mvdml Molegro Virtual Docker ere File Edit View Rendering Preparation Docking Tools Window Help W Q n wo v v Hydrogens Fog Hide Residues Search Se items Options v le Workspace New Constraints 1 Docking Template 4 M Ring 12 M Negative Charge 2 2 Hydrogen Accept 7 M Hydrogen Donor 1 M Ligands 5 O Active 1sf_kpl_h LI 1srq_kpl_h 1sth_kpl_h Value Figure 99 Visualization of template groups Notice the corresponding categories in the workspace explorer molegro virtual docker user manual 10 Template Docking page 153 251 When a docking template has been created a new category Docking Template appears in the Workspace Explorer The category can be expanded to reveal the different template groups it contains Using the context menu on the Docking Template category it is possible to edit or remove an existing docking template From the context menu it is also possible to choose Open in Molegro Data Modeller this allows you to test each ligand or pose in the workspace against the template the atom overlap for each template group center will be calculated and the resulting spreadsheet will be opened in Molegro Data Modeller All val
265. ur distance factor default 1 0 This factor determines how close the point of the initial simplex will be to the other randomly selected individuals in the population A factor of 1 0 causes the initial simplex to span the neighbour points exactly while a factor of 0 5 would correspond to simplex points being created halfway between the individuals chosen for optimization and its randomly chosen neighbours Notice that a factor less than 1 0 will converge slowly Typical values should be in the range of 0 95 to 3 0 To use the MolDock SE search algorithm the OPTIMIZERTYPE script command has to be set Moreover specific search algorithm parameters are set by the OPTIMIZER script command see Appendix XI Script Commands for more details molegro virtual docker user manual 30 Appendix XIII Iterated Simplex Iterated Simplex is an alternative search heuristic which can be used together with the Mo Dock and PLANTS docking scoring functions The algorithm works as follows First an initial population of poses is created initial number of poses is determined by the population size parameter Afterwards the following process will be executed until max iterations have occurred Each individual in the population will be refined using the Simplex local search algorithm also called Nelder Mead The Simplex algorithm will run for maximum steps or until the fractional difference between the best and worst vertices in the Simplex w r t t
266. used for the remainder Examples PREPARE maxIterations 4000 Use a higher number of iterations PREPARE runs 10 Multiple runs increases the accuracy of the poses found OPTIMIZERTYPE lt type gt The OPTIMIZERTYPE command sets the optimizer search function used while docking lt type gt is one of the following values MSE for the MolDock SE algorithm MolDock for the standard MolDock algorithm Simplex for the Iterated Simplex algorithm Notice MolDock SE is automatically set as the default optimizer Example OPTIMIZERTYPE MSE RANDOM lt seed gt Sets the seed used by the random number generator Normally this is not recommended since a random seed always is generated on startup but it can be used to reproduce docking runs since the seed is always recorded in the docking log RANDOM 123 Ensures that the simulation will always return the exact same results molegro virtual docker user manual 28 Appendix XI Script Commands page 239 251 SEARCHSPACE lt radius center gt Create a searchspace with a given radius and center position The center is based on a given molecule ligand cofactor pose or existing cavity Example SEARCHSPACE radius 12 center ligand 0 CONSTRAINTS lt integer list gt Per default all constraints defined in a MVD workspace are used The CONSTRAINTS
267. various graphical objects molecular surfaces backbone visualizations labels etc By default an empty workspace is shown when starting MVD A workspace can be saved cleared replaced by or appended to other workspaces The content of the current workspace is listed in the Workspace Explorer window which also allows for manipulation of the various items available see Section 3 4 for more details Notice When saving a workspace in the internal MVDML format not all 3D visualization objects are saved e g labels interactions annotations backbones and surfaces For more information about the MVDML format see Appendix VI Supported File Formats and Section 7 2 The user interface in MVD is composed of a central 3D view referred to as the Visualization Window or 3D world together with a number of dockable windows introduced below molegro virtual docker user manual 3 User Interface page 25 251 2 121p MYDML MYD2006 File Edit View Rendering Preparation Docking Window Help SOF i e Q C M ool bande Workspace Explorer x n e amp E ee bx A gt ma Visualization Window 4 o a o8 PEN 9 Properties 7 Vd 1AA Hydrogen b Acceptor Partial charge 0 5 Hybridization Temperature 0 Average an 0 Clear Selection Time Description 12 37 55 725 Macros loaded Console Wincow Figure 16 Main application window The MVD Toolbar provides easy and fast a
268. virtual docker user manual 19 Appendix II PLANTS Scoring Function page 206 251 and is included here in order for PLANTS scores to be comparable with the original PLANTS implementation The implementation of the PLANTS scoring function in MVD differs from the original PLANTS implementation in the following two cases 1 The original PLANTS implementation ignores default parameters for the Tripos torsional potential when handling dummy or S o2 typed atoms This means that contributions for these atom types are not taken into account in the torsional potential By default the MVD implementation takes all atom types into account non matching types will use default settings as described by Clark et al CLARK 1989 2 The penalty term Csite used by PLANTS is not well suited for the MolDock Optimizer or the MolDock SE search algorithms By default this penalty term is replaced by penalty scheme where a constant penalty of 10000 is assigned to the total energy if a ligand heavy atom is located outside the binding site region defined by the search space sphere The settings for original PLANTS implementation can be used in MVD by adding the originalplants true parameter option to the EVALUATOR script command see Appendix XI Script Commands for more details In order to use the PLANTS scoring function choose Scoring function gt Score gt PLANTS Score from the Docking Wizard The following parameter can be set Incl
269. w context menu appears when clicking on an atom in one of the molecules Align This will align the molecules The atoms are aligned in the same order as they are selected that is the first selected atom in ligand 1 is aligned to the first selected atom in ligand 2 etc Therefore it is important to ensure that the selection order is correct and that no other atoms are selected Notice Only alignments with three selected atoms in each molecule are possible The Macro and Menu Editor allows the user to modify existing menu entries or to extend the functionality by adding new menu entries It can be invoked by choosing Edit Macro and Menu Editor molegro virtual docker user manual 3 User Interface page 62 251 fA Macro and Menu Edito Macro overview Macro definition Macros Title Reset View RootFolder Label View hR E Hide from menu Hydrogen Bond Interactions Docking View Remove old objects Preparation View remove category ez remove category labels rophobicity l a atic Interactions remove category interactions remove category charges Pose Organizer View hide category annotations Secondary Structure View hide category surfaces Rendering hide category backbones Preparation Docking Make sure protein is visible show category proteins Execute Restore Macro Settings OK Figure 49 The Macro and Menu Editor The left pane Macro overview displays a hie
270. water cofactor molecules interacting with the inspected molecule a Show Atom Contributions which shows individual atoms in proteins cofactors and water molecules in the workspace interacting with the inspected molecule molegro virtual docker user manual 7 Analyzing the Docking Results page 122 251 The atoms residues and molecules are only displayed in the list if the interaction energy is greater then 0 3 in MolDock Score units As with the Ligand Atom Energy table selecting atoms residues or molecules in the table will select them in the 3D view and vice versa In addition it is possible to hide non selected residues by toggling on the Hide Non Selected Residues check box The energy contributions are also divided into the same categories as in the Ligand Atom Table for instance EElec and Epair Ligand Energy Inspector 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR A 1HVR B LUO fot prssFJR TTT LLLA Copy tables to clipboard Figure 81 Targets tab page The Total Energy Tab The Total Energy tab displays a hierarchical breakdown of the various energy contributions molegro virtual docker user manual 7 Analyzing the Docking Results page 123 251 When using the PLANTS scoring function the following columns are shown
271. will be loaded on startup The controller must be kept running in order to distribute jobs to the agents If the controller is closed no further jobs are sent to the agents It is possible to restart the job after the controller has been closed In order to do this start the controller e g from MVD using the Tools Virtual Grid Controller or using the command line virtualgrid exe controller The controller is able to resume the execution of pending units and completed units are not lost It is also possible to set a Controller ID This is useful if several people are running Molegro Virtual Grid controllers on the same network The Controller molegro virtual docker user manual 15 Molegro Virtual Grid page 186 251 ID is a simple text label that identifies the controller user to the rest of the network For instance when inspecting the running job units on an agent the controller ID is listed as the owner C Molegro Virtual Grid Controller File Agents Job Help Agent Status Job F Gridtests SampleDocking GridJob 7 192 168 1 152 Processing 2 units aes E 192 168 1 103 Idle Unit Status 0 Job has requested files 1 Job has requested files 2 In progress 3 In progress 4 Pending 5 Pending 6 Pending 7 Pending 8 Pending 9 Pending Pendina 10 Auto discover Add agents manually Clear list Pause job Remove job Combine results Time Descriptio
272. with 8 regions Figure 52 Energy Grid Visualization The MolDock GRID and PLANTS Score GRID scoring functions use a precalculated energy grid during the docking simulations to accelerate the protein ligand interaction calculations Visualising these potential fields makes it possible to gain an understanding of which regions are attractive to the atoms in a ligand Four different types of energy potentials can be shown Steric Favorable These are the regions where it is favorable to place non polar atoms These volumes are visualized in green This field will be strongest near the surfaces and in cavities Hydrogen Acceptor Favorable These are the spots where it is favorable to place a ligand atom capable of accepting a hydrogen bond i e spots near a hydrogen donor in the protein They appear as blue regions Notice that the fields do not take direction into account for instance the position of the hydrogen in a hydroxyl group is not taken into account when calculating the field it is assumed to be able to point in any direction Hydrogen Donor Favorable The regions show favorable spots for heavy atoms in the ligand that are able to donate a hydrogen to a hydrogen bond They appear in yellow Electrostatic Show the electrostatic potential of the protein Red molegro virtual docker user manual 3 User Interface page 66 251 regions correspond to a nearby negative electro static charge in the protein Blu
273. with id id SELECT ATOM selects closest atom to specified x y Z position molegro virtual docker user manual 27 Appendix X Console and Macro Commands page 222 251 SELECT RESIDUE selects residue with residue index icle SELECT RESIDUEID selects residue with internal residue index id SEED number Sets random seed It shows the current random seed if called without arguments STATUS Shows info about the objects in the workspace and Visualization Window Loaded modules are also listed SAVE filename Saves a MVDML file Do not include extension in filename LOAD filename Loads a MVDML file Do not include extension in filename CLS Clears console log CLEAR workspace selection CLEAR workspace removes all items in the current workspace CLEAR selection clears current selection HIDE hydrogens labels Hides either hydrogens or labels SHOW hydrogens labels Shows either hydrogens or labels FITTOSCREEN Fit all molecules in the visualization window Used for labeling objects This command is described in detail in the paragraph below ADDLABEL Notice It is much easier to use the Label dialog in the GUI GUI Commands SLAB near far Creates a slab slicing of the 3D world Notice The Clipping Planes dialog is easier to use QUALITY value Sets OpenGL rendering quality from O to 10
274. wo drop down menus The first Action provides a single option Set All Unknown to Default Protonation Invoking this option sets all residues with an unknown protonation to their default protonation state The second drop down menu Select provides an easy way to select multiple residues The following selections are possible Residues with Invalid Structure selects all residues with structural errors missing atoms or erroneous bonds Residues with Unknown Protonation selects all residues with protonation schemes not matched by any of the residue templates Finally the residues most likely to have a non default protonation state His Glu and Arg can be selected using this drop down menu Notice that the protonation templates are user customizable See the last section Customizing the protonation templates for more information molegro virtual docker user manual 4 Preparation page 76 251 In order to mutate change the residue type select a single residue from the list it is not possible to mutate multiple residues at once Whenever a new residue is chosen from the Mutate to drop down list the sidechain is replaced and the 3D view is updated to reflect the changes Current selected residue Select a single residue Mutate to Ala Figure 57 The residue mutation and optimization tab Residues are substituted by taking the corresponding template defined in the misc data residuetemplates mvdml file
275. ydrogen acceptors atoms form a template group Each template group contains a number of centers optimal 3D molegro virtual docker user manual 10 Template Docking page 149 251 positions for the group feature Figure 96 Example of a template with two groups ring atoms yellow and hydrogen donor atoms purple The colored spheres indicates group centers If an atom matches a group definition e g is a hydrogen acceptor it will be rewarded depending on its distance to the group centers by using the following Gaussian formula for each center e w exp d r 7 where d is the distance from the position of the atom to the center in the group is a weight importance factor for the template group and rois a distance parameter specifying a characteristic distance for the template group when d is equal to this characteristic distance the interaction is at e 36 of its maximum value and ro can be customized for each template group The following strategy applies when evaluating ligands during docking For each atom in the ligand score contributions from all centers in all matching groups are taken into account i e a single atom may contribute to several centers in several groups an atom is not restricted to the closest matching center or a single group The template score is normalized the resulting score found using the procedure above is divided by the score of a perfectly fitting ligand i e

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