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1. Binding Affinity coefficients misc data BindingEnergyCoefficients bt Pose Name The name of the ligand this pose was created from The name this file was stored as if any The energy score used during docking arbitrary units The estimated binding affinity kJ mol The reranking score arbitrary units The RMS deviation from a reference ligand f available gt Figure 55 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 optimal 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 The Re Evaluation of Poses Panel The middle panel allows for recalculation of scoring functions including MolDock molegro virtual docker user manual 6 Analyzing the Docking Results page 67 129 Score Binding Affinity score and re ranking score These scoring function values are already calculated if the poses are imported from a mvdresults file Pressing the Recalculate Energies button will recalculate the scores for each of the three measures using the coefficients specified in the files
2. ee to enforce all hard constraints and summarizes the soft TargetPose 3 constraint energy in the console 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 GETPDB lt key gt Downloads PDB with key 4 letter code from the Protein Data Bank ALIGN MoleculeTargeti 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 HIDE CATEGORY lt category gt Shows or hides Workspace Explorer category with given name i e SHOW CATEGORY water REMOVE OBJECT id Removes a 3D object from the world REMOVE moleculetarget Removes an object from the workspace TRANSLATE x y Z Moves active ligand ROTATE x y z angle Rotates active ligand molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 105 129 CD Print current directory DIR Shows dir of MVDML files in current directory PREV Loads previous MVDML file in current directory NEXT Loads next MVDML file in current directory VALIDATE Performs a validation of the complex RMSD Invokes RMSD dialog CAV Invokes Cavity detection dialog EVALUATOR initstring Sets
3. 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 molegro virtual docker user manual 10 Script Interface page 85 129 Notice The Python wrapper requires Python 2 4 or above The following example is taken from MVD2006 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 I0Error could not create path outputPath Now start the wrapper Remember to change the path to the executable in the line below mvd MvdWrapper MvdWrapper C Program Files Molegro MVD2006 bin mvdconsole exe gui True mvd info testing mvd random 123232 set the seed mvd cd outputPath change to output path 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 mv
4. molegro virtual docker user manual 3 User Interface page 24 129 The Workspace Explorer can also be used to inspect molecules in the Visualization Window using the left mouse button to select the molecules or 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 Ctri Shift when clicking on a molecule hydrogen bonds are shown for the selected molecule and non relevant protein residues are hidden 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 The Proper
5. 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 occurrence in the list molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 104 129 Command Description SET active reference targetligand Set active or reference ligand A lot of operations e g some surfaces are only performed on the active ligand The reference ligand is used to calculate RMSDs while docking EXPORT moleculetarget Export as Mol2 or PDB A File export dialog is opened for selection of a filename Can be used to test the current visible constraint It tries
6. Time Description 09 31 27 539 Solid surface created Hiding molecules in workspace Changed hydrogens view to show only polar hydrogens 09 33 03 026 Changed hydrogens view to show all hydrogens v 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 Afterwards use the Macro and Menu Editor described in Section 3 7 to explore which console commands that are used for a particular view molegro virtual docker user manual 3 User Interface page 28 129 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 click and selecting Set as Rotational Center Another option is to choose Fit to Screen from the Workspace Explor
7. 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 20 Appendix X Script Commands page 121 129 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 DOCK Docks the ligands in 3PTB MVDML and calculate their RMSD deviation from ligand 1 which is the second ligand present in the workspace 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 fi
8. Figure 50 Any warnings or errors are shown on the last page in the wizard 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 50 Setup Dockin In the final tab see Figure 53 two 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 10 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 molegro virtual docker user manual 5 Docking Functionality page 61 129 docking simulation on other computers The Output directory specifies where the docking data MVD script file MVD script log file docking results file and found poses will be stored The MVD script file script mvdscript
9. Pose Organizer Name Ligand MolScore Affinity Rerank Score HBond 00 XK2 XK2_263 242 796 30 6705 186 316 15 5613 _ Dynamic update notice disables multiple poses selection C Only showtop 1 poses for each ligand Sorting criteria 1st Name 2nd MolScore Pressing OK will keep 3 poses Figure 13 The predicted poses The Pose Organizer 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 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 molegro virtual docker user manual 2 Docking Tutorial page 19 129 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 Turn off the original ligand and the search space sphere colored green in the 3D view window by clicking the Ligands and Constraints
10. 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 f all hydrogens should be created Figure 3 Preparing the PDB file Notice If the protein structure has been prepared beforehand and saved in a format capable of handling all structural information 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 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 Now click the Import button The protein and the ligand appears in the Visualization Window see Figure 4 molegro virtual docker user manual 2 Docking Tutorial page 11 129 MYD2006 File Edit View Rendering Preparation Docking Window Help g ay Q itl x ad Hydrogens Fog Hide Residues items Options 7 Workspace New Ligands 1 Proteins 2 Properties x Property Value x Time Description 08 48 28 541 Preparing 1HVR A from file C Programmer Molegro MVD
11. Create Ligand Atom Constraint Define ligand constraint This Ligand Constraint is bound to ligand 0 BTN_300 Constrain the following atoms in ligand comma separated list of ID s f 115 Ligand constraints are specific to one ligand Soft constraint Penalize chosen atoms for making contacts Energy penalty 500 Reward atoms for making contacts Energy reward 500 Figure 43 Ligand Atom Constraint dialog 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 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 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 molegro virtual docker user manual 5 Docking Functionality page 54 129 Al anco Which Iidgandec tn Dank Choose Which Ligands to Dock oS The first action is to choose which ligands to dock see Figure 44 Docking Wizard Choose Which Ligands to Dock items
12. 0 0 6 1 5 sp sp n 3 3 0 Table 5 Torsional parameters molegro virtual docker user manual 12 Appendix II Docking Search Algorithm The docking 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 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 is 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 65 below shows an outline of the evo utionary process taking place in EAs molegro virtual docker user manual 12 Appendix II Docking Search Algorithm page 91 129 Initialization Mutation Recombination Figure 65 Outline of evolutionary algorithm The guided differe
13. BENCHMARK SMVDML mvdml RMSD ligand 0 DOCK 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 water tru OPTIMIZER cavity true popsize 50 crossoverrate 0 9 keepmaxposes 5 molegro virtual docker user manual 10 Script Interface page 84 129 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 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 been interpreted A small Python wrapper is provided in MVD2006 Scripting Python MvdWrapper py The wrapper encapsulates the various script commands in a small object MVDWrapper
14. cavities found are then ranked according to their volume molegro virtual docker user manual 14 Appendix IV Clustering Algorithm The multiple poses returned from a docking run are identified using the following procedure a During the docking run new candidate solutions poses scoring better than parental solutions see Appendix II Docking Search Algorithm 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 initial 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 cre
15. 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 a 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 Biased and randomized orientation Randomization of ligand orientation can be toggled on and off by setting the Randomize ligand orientation in the Docking Wizard If randomization of orientation is not enabled the docking search algorithm will be biased towards the orientation of the input ligand to be docked Notice Using the biased orientation can be advantageous if the orientation of the ligand to be docked is known beforehand or if the orientation is somewhat similar to the input structure For instance if another inhibitor is known it can be used to align the ligand to the inhibitor before the docking run is started see Section 6 5 for more details In these cases a biased orientation will allow the docking search algorithm to focus more on that specific orientation or nearby orientations leading to more accurate docking results a Ranking poses The most promising poses returned when the docking run terminates can be further analy
16. 10 4 Running the Script Interface Interactively ccceeeeee eee eeee 84 10 5 Running the Script Interface From Python cccccceeeeeeeeeeees 84 11 Appendix I Docking Scoring Function ssssssssrsssrrsnnassnrrsrrrnnns 86 12 Appendix II Docking Search AlgorithM sssssssssssrrssnrsrrrrsrrensnse 90 13 Appendix III Cavity Prediction sssssssrssrrrsrrrnrrsrnrrsrrrsrrrrnrrne 93 14 Appendix IV Clustering AIGOrithm cccccceeeeessseceeeeeeennnsaeees 94 15 Appendix V Supported File Formats cccccccseeeeseeeeeeeseneenenaaes 96 16 Appendix VI Automatic Preparation cccccceceseeeeeeeeeeeeneneneeaaas 98 17 Appendix VII Third Party CopyrigGhts cccccccceeeeeeeeesaeeeeeees 100 18 Appendix VIII Keyboard Shortcuts sssssssssrrssssrrnrrsrnnrrsnnrrne 102 19 Appendix IX Console and Macro COMMANGG cccceeeeeeeeeeeeees 103 20 Appendix X Script CommandS scstctioncecartensserrnercresretacieisntwcs 110 20 1 List of Script Commands Available s ssssssssssnnrnsrrrsrrrnrren 111 20 2 Flow Control s sssssssssssnnnssnrrsrrrnrrrsnrrrnrrnrrrrnrrennrssrrrnrrnnnnn 121 21 Appendix XI MolDock SE execs sescsccsed es naseesSesxevassancccuctateeucncdedeste 124 22 Appendix XII MolIDock Score Grid ccccccccceeeee eee eeesaaeeeeeees 127 23 Appendix XIII RETEPENCES sccccidecieseescccnddesiareceseliduessasadeeneieciaeays 129 molegro virtual docker user manual 1 I
17. 45 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 molegro virtual docker user manual 5 Docking Functionality page 56 129 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 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 46 Figure 46 Example of search space region green sphere 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 47 In order for a constraint to be meaningful it must be defined within the current search
18. 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 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 molegro virtual docker user manual 6 Analyzing the Docking Results page 65 129 window This setting is useful for quick comparison of different poses 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 When inspecting
19. Grid is a grid based version of the MolDock Score function It precalculates potential energy values on an evenly spaced cubic grid in order to speed up calculations Notice that unlike the standard MolDock Score the grid version does not take hydrogen bond directionality into account hydrogen bonding is determined solely on distance and hydrogen bonding capabilities The energy potential is evaluated by using tri linear interpolation between relevant grid points The rest of the terms in the MolDock Score Grid version i e internal ligand energy contributions and constraint penalties are identical to the standard version of the scoring function 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 A 0 4 A will be adequate in most cases Look out for the estimated memory usage in the Docking Wizard As a rule 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 MolDockScore grid version select it as the evaluation function in the Docking Wiza
20. Ligands BTN_300 Structural Water Proteins 1STP v Cancel Figure 44 Select which ligands to dock If more than one ligand is available 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 at a time Structural waters and cofactors if any are always included in the docking 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 with 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 44 e Scoring Function and Define Binding MVD includes MolDock Score E UOWEEN 2006 and a grid based version called MolDock Score Grid for evaluating docking solutions The MolDock Score is further described in Appendix I Docking Scoring Function The MolDock Score molegro virtual docker user manual 5 Docking Functionality page 55 129 Grid is identical to the Mo Dock Score except tha
21. Waals term between atoms and another stronger potential for hydrogen bonds The linear potential is defined by the following functional form Ep p O Ag Epip R1 0 Eprp R2 Epip R3 A Ep p r 0 forr R3 and is linearly interpolated between these values The parameters used here see Table 3 were adopted from GEMDOCK YANG 2004 Ao A Ri R2 R3 R3 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 3 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 4 molegro virtual docker user manual 11 Appendix I Docking Scoring Function page 88 129 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 structural water nonpolar all other atoms Table 4 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 Hfactor is Multiplied to the PLP hydrogen bond strength Hractor O Zp n 0 90 100 D Zn a aa 909 100 Zp 4 44 90 150 Here AA Acceptor Antecedent denotes a heavy atom connected to the acceptor A D denotes the donor and H
22. Window hide non selected residues change between one and three letter residue names and toggle details about secondary structure MVD2006 File Edit View Rendering Preparation Docking Window Help b Q tc items Options Workspace New CO Cofactors 2 tf O Ligands 1 Proteins 2 1HVR A 1HVR B Sequence Viewer Figure 26 Sequence viewer with selection of four residues highlighted in the Visualization Window The Sequence Viewer dialog can be invoked by selecting Window Sequence Viewer or using the Ctrl Shift S keyboard shortcut molegro virtual docker user manual 3 User Interface page 34 129 3 12 Workspace Properties 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 and Window Workspace Properties see Figure 27 Workspace Properties Workspace title 1407 Last saved not set _ Show properties window when loading workspace Workspace notes Here you can write comments and notes Figure 27 Workspace Properties dialog 3 13 Measurements and Annotations Distances and angles can be measured directly in the 3D world see Figure 28 If two atoms are selected the distance betwee
23. ana EEE aE Ra 35 3 15 Creating Molecular Surfaces ccccccceecenseeeeeesseseeeneeeseeesaans 37 3 16 Creating Protein BackboneS ssssssssssssrrrnssrrrnssrnrnssnnrrssnnrns 38 3 17 Making ScreenshotsS s sssssssssssrrrnssnnrrssnrrrssnrrrnrnrrerennnnrrnns 40 4 Preparati Mesrine aea E EADE E EAT 42 4 1 Import of MoleculeS ssssssssrrnrrssnrrsrrrnnnrrsrrrnrrsnnnrrnrrsrrrnnnrne 42 4 2 Automatic PrepalatloMubiniisccvsenunsancadsdverteawdetenaarseusdsiuicntesenivees 43 4 3 Manual Preparation ssssssssssssrrrssssrrnnrnnnnrrsnnnrrennrrrnnnnrressne 45 4 4 Protonation WIZOlO ccccteneseeenetcntenetiacedseeesdauuazeseerersenenereesseass 47 5 Docking Functionality ssssssssssssssrsssnrrrssnrrrssnrrrnrnrrrnrnnrnnrsnnnrens 49 5 1 Cavity Prediction ss ssssssssssrrenssrrrnssnnnrrsnnrrrssnnrnnrnnrnnrnnrarrene 49 9 2 CONSE AIAG oieee ssi E E T E 50 5 3 Docking Wizard sssssssssssunrrrsrsrrrnssrrnnssnnnrrsnnnrrsnnnrrennnrrrann 53 6 Analyzing the Docking ReSuIts ccccccccsssceeeeneseeeessesseeenaneeeenuanes 64 molegro virtual docker user manual page 4 129 6 1 Pose On Ca elec rat tua tamanmesecmansiasinansssianan ida mans Mon asldnoanseemmeaiesnaniais 64 6 2 Saving Molecules and Solutions Found sssssssssrssrrrsrrsssns 69 6 3 POSS I OG IMS cacacacnsvanwag antaneda ons E Ei Aa EAE E wadamaeea Gaa 70 6 4 RMSD MatriX soisi neniaro icen eenei aa AA 70 6 5 Structural AlignMent sssssssssss
24. and invoke the Docking Wizard The Docking Wizard guides the user through the different settings for the simulation 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 10 Script Interface page 82 129 Example mvd docktest mvdscript This will spawn the Script Progress GUI with information on how the script parsing is progressing E Molegro Virtual Docker Batchjob Running Batchjob started to 4 maj 10 46 28 2006 Elapsed 0
25. check boxes in the Workspace Explorer The poses in the Pose Organizer can be visualized by selecting them see Figure 14 2 Pose Organizer File Edit Table Settings Poses Name Ligand MolScore Affinity Rerank Score HBond CZ 00 XK2 XK2_263 242 796 30 6705 186 316 C2 01 XK2 XK2_263 203 952 29 7885 131 966 02 XK2 XK2_263 193 102 31 1972 145 564 C Only show top 1 m poses for each ligand Sorting criteria Ist MolScore 2nd None v 3rd None Pressing OK will keep 3 poses Figure 14 Viewing multiple poses 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 molegro virtual docker user manual 2 Docking Tutorial page 20 129 5 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 6 1 for more details This concludes the tutorial molegro virtual docker user manual 3 User Interface The user interface in MVD is com
26. 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 Assign Bonds This option allows to determine which atoms are connected covalently bound Two atoms are connected if their distance is more than 0 4 and less than the molegro virtual docker user manual 4 Preparation page 45 129 sum of their covalent radii plus a threshold of 0 45A the threshold is set to 0 4852 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 allows 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 geometri
27. 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 SDF 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 6 1 for more details Finally each pose is stored in SDF format These files are used by the Pose Organizer to show the 3D conformations of the poses in the Visualization Window Docking Wizard Setup Docking Execution Choose how to execute the docking Run docking in separate process Creates 3 scqpt and executes f in an extemal process You can continue working on the current workspace Create a docking scriptiob but do not run it now Can be used fo prepare larger docking runs e g on several machines Data output Output directory C Program Files Molegro MVD2006 DockingOutput The generated script the logfile and the found poses will be stored in the output directory Figure 51 Setup docking execution Finally when the Start button is pressed the docking run will start and the Molegro Virtual Docker Batch
28. cropdistance 0 hbond90 true water tru 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 function used while docking lt type gt is one of the following values MolDockGrid for the grid version of the evaluator MolDock for the standard version Notice MolDock is set automatically as the default evaluator Example EVALUATORTYPE MolDockGrid molegro virtual docker user manual 20 Appendix X Script Commands page 116 129 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 II Docking Search Algorithm Appendix XI MolDock SE or the section about the Docking Wizard where the parameters also 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 scalingfactor double 0 50 crossoverrate double 0 90 offspringstrategy int 1 earlytermination double 0 01 terminationscheme int 0 randomizeligand true false Determines whether the ligand or
29. 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 17 Appendix VII Third Party Copyrights page 101 129 Icons The icon set used in MVD 2006 is taken from The Tango Icon Library http tango project org They are released under the Creative Commons Share Alike license http creativecommons org licenses by sa 2 5 molegro virtual docker user manual 18 Appendix VIII 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 Z CTRL Y CTRL Q CTRL 1 to 8 F1 to F9 Import Molecules Open Workspace Clear Workspace Save Workspace Toggle full screen Toggle dockable windows Toggle Cofactors category on off Toggle Ligands category on off Toggle Proteins category on off Toggle Water category on off Undo Redo 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 19 Appendix IX Console and Macro Commands When using the Macro and Menu Editor or entering commands in the console the following commands can be used
30. for the binding affinity and re ranking scores The ranking score function is computationally more expensive 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 The binding affinity is believed to be the best choice when trying to identify the best binder to a given target between a set of different ligands The binding affinity of a given pose is given by Ebinding 5 68 pKi and is measured in kJ mol the numerical factor corresponds to a temperature of 297K The pKi is predicted using a combination of energy terms and molecular descriptors and then converted to a binding affinity estimate using the equation above The coefficients for the binding affinity terms were derived using multiple linear regression The pKi estimator has been calibrated using a data set of more than 200 complexes with known binding affinities The correlation coefficient was 0 60 when doing 10 fold cross validation In general estimating the binding affinity is a difficult task Although the accuracy of our binding affinity estimation is on par with other approaches our current implementation is considered a work in progress and we expect to improve it further The bottom panel Table columns determines whi
31. 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 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 43 It is possible to modify the list of atoms in the ligand by entering a comma separated list of IDs molegro virtual docker user manual 5 Docking Functionality page 53 129 Notice Ligand Atom Constraints are always soft constraints It is possible to choose whether the chosen atoms in the ligand should be rewarded or penalized for contacts with the target molecules proteins cofactors and water 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
32. import a O aes 0 2 g Proteins 2 2 1HVR A 920 atoms 1HVR B 920 atoms Ligands 1 1 XK2_263 46 atoms Import small molecules as Ligands Replace or add to workspace Add to current workspace Y 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 these 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 10 129 Import Molecules Import Preparation Wamings 0 Assign All Below Custom Assign bonds if Missing Assign bond orders and hybridization F Missing Create explicit hydrogens if Missing Assign charges Always Detect flexible torsions in ligands Notice Always The preparation options F Missing Always Never Remove applies to each individual molecule not each individual bond or atom For instance setting
33. initstring for evaluator OPTIMIZER initstring Sets initstring for optimizer DUMP ligand pose ligandenergy poseenergy torsiontree Shows various debug info about structure EVAL all hbond esbonds EVALLIG all hbond esbonds EVAL evaluates the energy of the active ligand If all is specified hbonds and electrostatic interactions are visualized If hbond is specified hbonds are visualized If esbonds is specified electrostatic interactions are visualized EVALLIG evaluates the current pose can be used while docking SELECT ID lt id gt SELECT ATOM lt x y z gt SELECT RESIDUE lt id gt SELECT RESIDUEID lt id gt Selection of objects SELECT ID selects all atoms with id id SELECT ATOM selects closest atom to specified x y Z position SELECT RESIDUE selects residue with residue index id 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 molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 106 129 SAVE filename Saves a MVDML file Do not include extension in filename LOAD filename Loads a MVDML file Do not include extension in filename AD
34. is the donated hydrogen atom The ramp function is defined as D AjAmin Amax O for ASAmin and A Amin 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 hydroxyl 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 Entra is the internal energy of the ligand E ata X Ji r F X All 7 cos m 0 0 T E sini ic ligand jeligand flexible bonds 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 5 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 term Eciash assigns a penalty of 1000 if the distance between two heavy atoms molegro virtual docker user manual 11 Appendix I Docking Scoring Function page 89 129 more than two bonds apart is less than 2 0 A Thus Esas term punishes infeasible ligand conformations Oo m A sp sp
35. 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 MolDock evaluator and optimizer can be modified using the EVALUATOR and OPTIMIZER commands 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 Changes the current working directory to the given path molegro virtual docker user manual 20 Appendix X Script Commands page 114 129 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 ligandes true false Determines whether the internal electro static energy of the ligand should be included 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 t
36. 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 Ctri 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 Extended debug is enabled for them These items won t show up in the menus unless Extended GUI debug properties is enabled in the Preferences 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 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 Currently rearranging the macros e g changing the order of occurrence within a macro folder or moving macros between folders is not supported in the Macro and Menu Editor Instead these modifications can be done by manually editing the macros xm1 file containing the macro definitions located in the Data directory If some macros are deleted or modified by mistake the default macro settings can be restored by pr
37. requires that the energy has been evaluated using the eval command Torsion Tree Labels Syntax Label tree string Torsion Tree labels are evaluated at each rigid component of the ligand EA EA EA shows the Atom Energy of the rigid component EA shows the difference between this energy for the pose and for the molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 109 129 ligand It is only well defined on poses EB EB EB shows the Bond Energy of the rigid component EB shows the difference between this energy for the pose and for the ligand It is only well defined on poses ETOT ETOT Shows the total energy of the rigid component of the tree This requires that the energy has been evaluated using the eval command ETOT shows the difference between this energy for the pose and for the ligand It is only well defined on poses The depth of the torsion tree Higher values indicate that the rigid component is built later ele The rigid root component will have depth 0 Optimal placement of the rigid root will result in a lower maximum depth BOND Shows the bond index that this rigid component rotates about ID Internal index ATOMS Number of atoms in rigid component Residue Labels Syntax Label residue string ID Internal residue index LONGNAME Full residue name histidine cysteine NAME 3 lette
38. set to double 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 17 Appendix VII 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 identified 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
39. space region molegro virtual docker user manual 5 Docking Functionality page 57 129 Docking Wizard Enable or Disable Additional Constraints Constraints B Constraints 2 Distance Constraint Type By ID Hard Ligand Atom Penalty Constraint on ID s 12 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 47 Enabling or disabling user defined constraints rch Algorithm Choose The default search algorithm used in MVD is the Mo Dock Optimizer THOMSEN 2006 From MVD v1 5 an alternative search algorithm named MolDock SE simplex evolution is available MolDock SE 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 The MolDock SE algorithm and its parameters is further described in Appendix XI MolDock SE Notice MolDock SE is still experimental as all parameters has not been fine tuned yet Although it should be stable it is still to be considered a technology preview version 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 h
40. your application Figure 1 Check for updates molegro virtual docker user manual 2 Docking Tutorial This tutorial will go through a simple redocking scenario highlighting aspects such as import and preparation of molecules conducting the actual docking run and visual inspection of the poses found 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 The Import Molecules dialog see Figure 2 appears molegro virtual docker user manual 2 Docking Tutorial page 9 129 Import Molecules Import Preperation Wamings 0 Select which molecules to
41. 0 00 13 Finish estimated 10 50 58 Remaining 00 03 45 Working path c Program Files Molegro MVD2006 ScriptOutput Current ligand 1 truns 0 Log Poses current ligand Poses all Graph Skip ligand Time Ce ene er ed 10 46 29 304 10 46 29 304 10 46 29 304 10 46 29 314 10 46 29 314 10 46 29 314 10 46 29 314 10 46 29 344 10 46 29 374 10 46 29 384 10 46 34 151 10 47 06 237 10 47 06 357 Description I UIJ RU VOIA IUN Ivu U Found grid in workspace Setting evaluator init string cropdistance 0 hbond90 true Setting optimizer init string cavity truepopsize 50 scalingfactor 0 50 crossoverrate 0 9 The random seed used for this session is 1710097600 Optimizer Pop Size 50 ScaleF 0 5 PC 0 9 OffStrategy 1 earlyTerm 0 01 SW 0 ForceCa useEPenal useElntra Creating Docking Results file c Program Files Molegro MVD2006 ScriptOutput Docki Evaluator TorsionScheme 1 dampFactor 1 cropDistance 0 Docking ligand XK2_263 Beginning run 1 out of 1 Source Ligand was randomized This will destroy its original orientation Paused script Resumed script Evaluations s 55 0888 Accumulated 2035 v Status Running Figure 64 Script Progress GUI 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 withou
42. 2006 examples 1HVR pdb gt 03 48 28 851 Preparing 1HVR B from file C Programmer Molegro MVD2006 examples 1HVR pdb pz 08 48 28 951 Preparing XK2_263 from file C Programmer Molegro MVD2006 examples 1HVR pdb 8 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 Las Workspace Explorer tems B Workspace New Figure 5 Hiding the Protein Now zoom in on the ligand see Figure 6 molegro virtual docker user manual 2 Docking Tutorial page 12 129 Zooming can be performed using either a the scroll wheel on the mouse a 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 the protein We will do this by choosing Create Surface from the Proteins context menu in the Wor
43. D BACKBONE radius Adds a backbone a bezier spline through the backbone carbons ADD CHARGES Shows spheres around charged atoms ADD P SURF radius resolution probesize ADD P SURF LIGAND resolution probesize Adds a molecular surface Notice It is much easier to use the Surface dialog in the GUI If prepended by p the surface will be colored by electrostatic potential If followed by the surface will carved a Connolly surface We recommend the carved surfaces for best visualization If not followed by existing surfaces will be removed If no radius is given the surface will cover the protein If a radius is given the surface will cover the protein in the given radius but centered at the current active ligand If the variant with LIGAND argument is used the surface will cover the currently active ligand Resolution is typically 0 4 0 9 Don t choose higher resolutions i e lower than 0 4 unless you are prepared to wait for a long time The default value of the probesize 1 2 should be fine for most purposes Examples ADD PSURF 10 Electrostatic carved protein surface with radius 10A centered at the active ligand ADD SURF ligand 0 4 Carved ligand surface with resolution 0 4 DELETE Charges HBOND Labels Poses Deletes specified objects LIST POSES Shows all poses with info about parameters CLS Clears console log CLEAR workspa
44. Keyboard shortcut Ctn 2 C Extended debug only Preparation View Hydrophobicity Electrostatic Interactions remove category guides Pose Organizer View remove category labels f Secondary Structure View Reset View Rendering Preparation Docking 5 Misc hide category surfaces hide category backbones hide category annotations remove category interactions remove category charges light 0 on 0 0 6 0 9 30 40 30 light 1 on 0 0 8 0 9 30 40 30 color ligand fixed 1 1 1 color pose fixed 100 style protein wireframe 0 15 0 15 ahida linsead atid O90 T Figure 22 The Macro and Menu Editor It can be invoked by choosing Edit Macro and Menu Editor or Window Macro and Menu Editor The left pane Macro overview displays a hierarchical 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 molegro virtual docker user manual 3 User Interface page 30 129 A macro consists of a Title which is the name that is shown in the corresponding
45. Ligand Efficiency 2 Binding Affinity divided by Heavy Atoms count LE3 Ligand Efficiency 3 Rerank Score divided by Heavy Atoms count Table 1 Column names available in the Pose Organizer dialog molegro virtual docker user manual 6 Analyzing the Docking Results page 69 129 6 2 Saving Molecules and Solutions Found Saving Workspace After importing and preparing molecules all information can be saved ina 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 cavities interactions state information active and reference ligand structural water enabled disabled are not saved in MVDML files Exporting Molecules The Export Molecules dialog can be used to export all or a selection of the molecules available in the workspace see Figure 56 e Export Molecules ae Molecules Water 84 Proteins 1 1STP 1741 atoms Ligands 1 BTN_300 30 atoms E Notice Proteins and waters cannot be exported to MDL Mol files sdf sd mol mdl Output scheme One single file Figure 56 Export Molecules dialog Select which molecules to export To export molecules select File Export Molecules or Export
46. 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 MDL Mol files molegro virtual docker user manual 6 Analyzing the Docking Results page 70 129 Exporting Poses Found 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 6 3 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 58 When invoking the Pose Modifier a new pose is created Pose Modifier Dynamic Update Minimization RotVector 1 1 RotVector 2 0 RotVector 3 0 RotAngle 0 Reset All to Defaults Apply Figure 57 Pose Modifier dialog LJ Notice It is not possible to directly modify poses after the workspace has been 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 6 4 RMSD Matrix 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 Ato
47. 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
48. The Graph tab shows the convergence of the population of candidate solutions The blue graph shows the energy of the best pose and the red graph shows the mean energy of the entire population of candidate solutions see Appendix II Docking Search Algorithm for more details about the docking simulation and the population terminology molegro virtual docker user manual 5 Docking Functionality page 63 129 Molegro Virtual Docker Batchjob Finished Batchjob started to 31 aug 09 07 45 2006 Elapsed 00 01 48 Skip run Finish estimated 09 11 37 Remaining 00 02 03 Working path C Program Files Molegro MVD2006 DockingOutput Current ligand 1 1runs 00000 0mm me 100 Log Poses current ligand 2 Poses all 2 956 26 576 03 Figure 53 Docking progress dialog with convergence graph shown molegro virtual docker user manual 6 Analyzing the Docking Results The Pose Organizer is used to inspect poses found see Figure 54 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
49. X Script Commands page 119 129 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 Notice MolDock is set automatically 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 INFO lt output gt Writes output to the console Can be useful for debugging loops Example INFO Variable ais Sa Outputs the value of Sa molegro virtual docker user manual 20 Appendix X Script Commands page 120 129 CONSTRAINTS lt integer list gt Per default all constraints defined in a MVD workspace are used The CONSTRAINTS 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
50. ant 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 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 molegro virtual docker user manual 8 Obtaining the Best Docking Results page 78 129 a Multiple runs Because of the stochastic nature of the docking search algorithm it is recommended to make multiple runs for each ligand 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 When conducting more than one docking run Randomize ligand orientation should be enabled see Biased Orientation bullet below Additionally it is recommended to ignore similar poses returned see Section 5 3
51. ated 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 14 Appendix IV Clustering Algorithm page 95 129 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 15 Appendix V 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 mo 2 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 remainder is ignored all file formats If one of the other alternatives should be used change the order of occurrence in the 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 exp
52. aving more than 15 flexible torsions or if no promising cavities exist If cavities have been identified see Section 5 1 the poses found by the search 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 Moreover randomization of ligand molegro virtual docker user manual 5 Docking Functionality page 58 129 orientation can be toggled on and off by setting the Randomize ligand orientation option If randomization of orientation is not enabled the docking search algorithm will be biased towards the orientation of the input ligand to be docked see Chapter 8 for more details 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 combination and setting the Number if runs to 50 The General Settings show the parameters used by the search algorithm The default values shown are generally suitable for most docking tasks However in some cases increasing the Population size to 100 can improve the performance of the docking proced
53. c 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 Docking 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 Always If this option is set to Remove the ligand will be considered rigid during docking Atom hydrogen bonding types acceptor donor both or non polar are always set during preparation Molecules can be manually prepared using the context menus of highlighted atoms or bonds see below molegro virtual docker user manual 4 Preparation page 46 129 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 Hydrogen bond type 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 The Set Hydrogen Count menu option can be used to set the number of explicit hydrogens attached to the highlighted atom Currently the MVD scoring function MolDock Score see Appendix I Docking Scoring Function for more details uses partial charges assigned when
54. ce selection CLEAR workspace removes all items in the current workspace CLEAR selection clears current selection HIDE hydrogens labels Hides either hydrogens or labels molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 107 129 SHOW hydrogens Shows either hydrogens or labels labels FITTOSCREEN Fit all molecules in the visualization window Used for labeling objects This command is described in detail in the paragraph below LABEL 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 LIGHT number on off ambient diffuse specular x y z Sets OpenGL light sources FOG LINEAR near far FOG EXP EXP2 exponent FOG OFF Sets OpenGL fog COLOR protein pose ligand water cofactor fixed cpk hbond hbond2 interaction interaction2 r g b Sets the color style of specified object STYLE protein pose ligand water cofactor vdw fixed stick none atomScale bondScale Sets the visualization style of specified object REBUILD Rebuilds all objects in the Visualizer Window This command is necessary to call after the visualization styles or coloring schemes have been updated Ot
55. ch columns descriptors that are shown in the table on the first tab Table 1 describes the descriptors that are available molegro virtual docker user manual 6 Analyzing the Docking Results page 68 129 Column Name Description Name Pose name Ligand The name of the ligand this pose was created from Filename The name this file was stored as if any MolDockScore The energy score used during docking arbitrary units Affinity The estimated binding affinity kJ mol Rerank Score The reranking score arbitrary units RMSD The RMS deviation from a reference ligand if available Interaction The total interaction energy between the pose and the target molecule s Cofactor The interaction energy between the pose and the cofactors Protein The interaction energy between the pose and the protein Water The interaction energy between the pose and the water molecules Internal The internal energy of the pose Solvation The energy calculated from the implicit solvation model Protein VdW Protein steric interaction energy from an alternative 12 6 VdW potential Torsions The number of chosen rotatable bonds in the pose Soft Constraints The energy contributions from soft constraints Electro The electrostatic energy in the model HBond Hydrogen bonding energy Heavy Atoms Number of ligand heavy atoms LE1 Ligand Efficiency 1 MolScore divided by Heavy Atoms count LE2
56. cript commands Examples This is a one line comment This is a commen spanning more than one line which can be useful when describing wha is going on on ae 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 Files imported using the IMPORT command are always prepared using currently set preparation settings See the PREPARE command Files are always appended to the workspace The workspace is not cleared You can clear the workspace using the NEW command If you want to import MVDML files use the LOAD command Ifa complete file path is not specified the current working directory is used to search for the files See the CD command Examples IMPORT Ligand 1 3 FROM testdock mol2 IMPORT All FROM testdock mol2 IMPORT Proteins Waters Cofactors FROM lhvr pdb molegro virtual docker user manual 20 Appendix X Script Commands page 112 129 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 IfM
57. d 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 SPDB mvdml RMSD ligand 0 DOCK NEW ENDFOR 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 molegro virtual docker user manual 20 Appendix X Script Commands page 123 129 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 SPDB 3PTB LOAD C BENCHMARK SPDB mvdml RMSD ligand 0 DOCK molegro virtual docker user manual 21 Appendix XI MolDock SE MolDock SE simplex evolution is an alternative search heuristic which can be used together with either the Mo Dock or MolDock 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 Notice MolDock SE is still experimental as all parameters have not been fine tuned yet Although it should be stable it is still to be c
58. d 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 MVD2006 Bin MVDConsole exe instead of mva MvdWrapper MvdWrapper C Program Files Molegro MVD2006 Bin MVD exe molegro virtual docker user manual 11 Appendix Docking 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 H tk score inter intra where Enter is the ligand protein interaction energy Eme E E pip ty 3320 3 ieligand je protein ij The summation runs over all heavy atoms in the ligand and all heavy atoms in the protein including any cofactor atoms and water mo
59. der will present a list of matches a maximum of 30 matches is returned It is also 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 MYD2006 File Edit View Rendering Preparation Docking Window Help 9 Ho ff gens Fog Hide Residues Ser 27 1STP Asp 36 1STP Ser 45 1STP Asn 49 1STP Ser 52 1STP Asp 61 1STP Ser 62 1STP w Figure 25 Workspace Finder dialog 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 molegro virtual docker user manual 3 User Interface page 33 129 The Workspace Finder is invoked by typing characters in the search box text field located in the far right side of the MVD Toolbar 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 The Sequence Viewer dialog see Figure 26 allows you to inspect protein residues in an easy manner Using the context menu on the Sequence Viewer window it is possible to select residue atoms in the Visualization
60. e 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 40 129 Figure 35 An example of a protein backbone using the Tube graphics style It is also possible to set the color scheme for the backbone 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 m
61. e 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 180 the initial population would be biased towards the identity orientation i e no rotation To avoid this bias the algorithm by Shoemake et al GHOEMAKE 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 manual 13 Appendix Ill 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 whet
62. enu or hidden using the check box Screenshots can be made by choosing Window Capture Screen molegro virtual docker user manual 3 User Interface page 41 129 Capture Screen Image Area Visualization Window Format PNG 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 format 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 following file formats a Protein Data Bank pdb ent a Sybyl Mol2 mol2 MDL sdf sd mol mdl Notice that only PDB and Mol2 files can contain proteins cofactors and structural waters In general it is recommended to use Mol2 or SDF files for ligands since they usually contain bonding information From the Import Molecules dialog shown in Figure 37 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
63. er 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 la 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 29 129 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 3 7 Macro and Menu Editor The Macro and Menu Editor allows the user to modify existing menu entries or to extend the functionality by adding new menu entries Macro and Menu Editor Macro overview Macro definition Macros Title Docking View B RootFolder Label View Hydrogen Bond Interactions
64. ering all ring bonds remains a 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 Assign Hyb idization 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 docker user manual 16 Appendix VI Automatic Preparation page 99 129 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
65. erties Reset All to Defaults A Apply j Figure 61 The debug tab of the Preferences dialog For standard uses it is not recommended to change the default settings of any of these options The Create system log in Logs directory option is used to toggle whether a system log is created for each execution of MVD The system log contains information of user actions conducted and is used to track potential bugs and performance problems The log files are stored within the Logs directory located in the same directory as the mvd executable file Notice If you encounter problems with MVD please email the log file created before the crash to bugs molegro com 7 2 Command Line Parameters Currently the following command line parameters are available lt filename gt nogui interactive currentPath 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 MVD2006 bin mvd 1stp pdb 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 molegro virtual docker user manual 7 Customizing Molegro Virtual Docker page 75 129 The nogui parameter can be used to run the script job without invoking the progress dialog Example Molegro MVD2006 bin mvd mydocking mvdscript
66. essing the Restore Macro Settings link located in the lower left corner of the dialog Alternatively the macros xm1 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 IX Console and Macro Commands 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 a ligand deeply buried inside a macromolecule Far o o i Near 60 o I Figure 23 Clipping Planes dockable window molegro virtual docker user manual 3 User Interface page 31 129 Clipping Planes can be enabled by choosing Window Clipping Plane from the menu bar Clipping Planes are enabled when the Clipping Plane window is shown and disabled when it is closed Adjust the near and far slider until the desired region is shown The Hide Residues dialog see Figure 24 allows you to hide residues outside of a user defined sphere this can for example be used to show only the relevant residues near the binding site of the protein It is possible to set the center to of the sphere to the following objects if they are part of the workspace The center of the protein s the center of the Active Ligand the center of the Reference Ligand t
67. file typically SDF or Mol2 files a subset of the ligands can be selected for import using the Specify ligand range option See Figure 37 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 43 129 5 Import Molecules Import Preparation Wamings 1 Select which molecules to import 479 33 atoms 1004 25 atoms 1011 46 atoms 1012 46 atoms 1013 45 atoms 1042 22 atoms 1199 43 atoms 1424 16 atoms 1460 26 atoms 1482 43 atoms 1614 74 atoms 1684 30 atoms 1694 23 atoms to 2088 gt Ligands Replace or add to workspace Add to curent workspace Figure 37 Import Molecules dialog When all relevant molecules have been imported a minimum of one protein and one ligand is required the molecules can be automatically prepared see next section 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 It is important for MVD to dock correctly 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 all
68. 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 a The Ignore similar poses option is used to avoid reporting to similar 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 Docking Wizard Pose Clustering Multiple poses Retum multiple poses for each run Max number of poses retumed _ Enable energy threshold Cluster similar poses RMSD threshold Ignore similar poses for multiple runs only RMSD threshold Figure 49 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 molegro virtual docker user manual 5 Docking Functionality page 60 129 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 Docking Wizard Wamings Category Detailed description No errors or wamings
69. gand Define from selected atoms Hard constraint Require distance to be between Soft constraint Penalize distances with Piecewise Linear Potential term Energy penalty AO 20 00 A1 250 Distances A RO 2 30 R1 260 R2 310 S R3 360 20 00 mE 3 52 15 77 Figure 42 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 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 down menu The different choices for multiple atoms are All meaning all atoms None which causes molegro virtual docker user manual 5 Docking Functionality page 52 129 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 li
70. gand 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 Docking 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 potential 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
71. he center of any cavity in the project the center of the currently defined search space or the center of a selection of atoms if any The residues are dynamically disabled or enabled when the Sphere radius 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 contained in the sphere defined in the panel above the button corresponding to the type will be grayed and can not be toggled Select Which Residues to Hide Hide residues outside of a sphere with Sphere center Active Ligand v Sphere radius A 11 Only show the following residue types Ser Tp Tyr va C Backbone only Figure 24 Hide residues dialog The Backbone only check box can be used to toggle whether side chains are visible or not molegro virtual docker user manual 3 User Interface page 32 129 The Hide Residues dialog can be invoked by selecting Window Hide Residues Dialog or 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 or choose Window Hide Residues Dialog again The Workspace Finder located in the MVD Toolbar see Figure 25 allows you to quickly search for molecule names and residue atom IDs in the workspace When a name or ID number or part of it is typed in the search box the Workspace Fin
72. her 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 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 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
73. herwise graphical changes will not be reflected in the GUI The label 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 molegro virtual docker user manual 19 Appendix IX Console and Macro Commands page 108 129 To clear all labels use label without any argument VELED Description Atom labels Syntax Label string ID Internal atom index Hydrogen bond type non polar acceptor donor both The HBOND Type i variable below is probably of more use PC Partial Charge PC PC ignores atoms with no partial charge HYB Hybridization HYB only displays hybridization for atoms with other hybridizations HYB 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 Bond labels Syntax Label bond string ID Internal bond index Type Bond order single double triple aromatic Shows the total energy of the bond ETOT This
74. ientation should be randomized before each docking run keepmaxposes int 5 excludeenergythreshold double 10000 clusterthreshold double 0 0 The following parameters are used by the MolDock SE search 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 lowered to the quick try value simplexsteps int default 300 The number of iterations of the Nelder molegro virtual docker user manual 20 Appendix X Script Commands page 117 129 OPTIMIZER lt initstring gt Mead simplex minimization procedure performed at each step of the MolDock SE algorithm simplexdistancefactor double Default is 1 0 This factor determines how close the point of the initial simplex will be to the other ra
75. igand 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 Distance constraints constrain ligand atoms to a given position in 3D space see Figure 42 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 molegro virtual docker user manual 5 Docking Functionality page 51 129 Create Distance Constraint Constrained system Contraint center X DEA Y 1645 z 2229 gl Ligands are constrained to Specific ligand atom id oo a Ligand atoms of type Al v Specific atoms for each li
76. ign the protonation states only taking into account the positions of explicit hydrogens in the protein The other button Auto Protonate To Default Protonation State assigns a standard protonation corresponding to neutral pH i e histidine is protonated at the delta nitrogen The last panel Residue list shows a list of residues and their current protonation state If a residue is selected on the list the 3D view will focus on it HIO Unprotonated HIE NE2 Protonated v HID Default ND1 Protonated HIP Both Protonated 3D View Scale to Fit Figure 40 Example of possible protonation states for Hisitidine In the 3D world all relevant residues are displayed with a green sphere around them if the protonation state is erroneous or not supported the spheres will be red By using the context menu on these Protonation Guides an alternative protonation can be set The protonation states are important as they determine the hydrogen bonding capabilities of the protein and hence will affect the poses found and the docking energies molegro virtual docker user manual 5 Docking Functionality 5 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 III Cavity Prediction for details Cavity Prediction General settings Molecular surface WETEA v Max number of cavities 5 al Simple l
77. ill be molegro virtual docker user manual 2 Docking Tutorial page 15 129 stored Choose a directory pressing the button or keep the default settings gt Docking Wizard Setup Docking Execution Choose how to execute the docking Run docking in separate process Creates 3 sopi and executes f in an extemal process You can continue working on the current WorkSpace Create a docking scriptiob but do not run it now Can be used fo prepare larger docking mins E g on several machines Data output Output directory C Program Files Molegro MVD2006 PockingOutput The generated script the logfile and the found poses will be stored in the output directory Figure 10 Setup docking execution 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 molegro virtual docker user manual 2 Docking Tutorial page 16 129 E Molegro Virtual Docker Batchjob Running Batchjob started to 4 maj 10 46 28 2006 Elapsed 00 00 13 Finish estimated 10 50 58 Remaining 00 03 45 Working path c Program Files Molegro MVD2006 ScriptOutput Current igand 1 1 _ ESES S Log Poses current ligand Poses fall Graph Time 10 46 29 304 Found grid in workspace 10 46 29 304 Setting evaluator init string cropdistance 0 hbond90 true 10 46 29 304 Setting optim
78. important to ensure that the selection order is correct and that no other atoms are selected Alignments can be undone click the undo button in the tool bar Notice Only alignments with three selected atoms in each molecule are possible molegro virtual docker user manual 7 Customizing Molegro Virtual Docker 7 1 General Preferences Molegro Virtual Docker can be customized using the Preferences dialog which can be invoked from the Window or Edit menus or by pressing F4 Preference settings are categorized in General Graphics and Debug tabs Preferences e General Graphics Debug _ Load most recent workspace on startup f any C Check for new updates on startup Working directory C Molegro Pu Besa itio Deta C e Figure 59 First tab of the preferences dialog In the General tab see Figure 59 the following settings are available a The Load most recent workspace on startup if any option toggles automatic import of the last used workspace molegro virtual docker user manual 7 Customizing Molegro Virtual Docker page 73 129 a The Check for new updates on startup option enables MVD to automatically check for new updates during startup 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 The Graphics tab see Figure 60 con
79. ion speed significantly World Ar Changing the 3I The visualization engine is highly configurable Molecules can be drawn as lines wireframe ball and sticks capped sticks and space fill CPK molegro virtual docker user manual 3 User Interface page 26 129 1STP mvydml MVD2006 SE File Edit View Rendering Preparation Docking Window Help B so e Q re A X v Hydrogens Fog Hide Residues x Workspace Explorer Items Options Workspace New ia Ligands 1 Active BTN_300 O Proteins 1 Surfaces 1 p f Properties Froperty Value Selection Position 13 5621 0 0781 Atom ID 28 Element H 1 Clear Selection 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 3 User Interface page 27 129 MYD2006 File Edit View Rendering Preparation Docking Window Help SOP peat As Q igs e Hydrogens Fog Hide Residues items Options E Workspace New Backbones 2 a O Cofactors 2 O HYD_6 7 A O HYD_67 B O Ligands 1 O Active XK2_263 F Poses 1 Proteins 2 1HVR A 1HVR B Surfaces 1
80. is 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 molegro virtual docker user manual 12 Appendix II Docking Search Algorithm page 92 129 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 Only ligand properties are represented in the individuals since the protein remains rigid during the docking simulation Thus a candidate 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 th
81. issing 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 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 mvdmI 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 molegro virtual docker user manual 20 Appendix X Script Commands page 113 129 SAVE lt mvdml filename gt Save the current workspace as a MVDML file All molecular structures in the workspace are saved 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
82. 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 Protonation If the protein is expected to have unusual protonation states near the binding site be sure to set them using the Protonation Wizard 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 molegro virtual docker user manual 8 Obtaining the Best Docking Results page 77 129 The default settings listed in the wizard are generally applicable 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
83. izer init string cavity truepopsize 50 scalingfactor 0 50 crossoverrate 0 9 10 46 29 314 The random seed used for this session is 1710097600 10 46 29 314 Optimizer PopSize 50 ScaleF 0 5 PC 0 9 OffStretegy 1 earyTerm 0 01 SW 0 ForceCa 10 46 29 314 Evaluator TorsionScheme 1 dampFactor 1 cropDistance 0 useEPenal useEIntra 10 46 29 314 Creating Docking Results file c Program Files Molegro MVD2006 ScriptOutput Docki 10 46 29 344 Docking ligand XK2_263 10 46 29 374 Beginning run 1 out of 1 10 46 29 384 Source Ligand was randomized This will destroy its original orientation 10 46 34 151 Paused script 10 47 06 237 Resumed script 10 47 06 357 Evaluations s 55 0888 Accumulated 2039 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 molegro virtual docker user manual 2 Docking Tutorial page 17 129 Molegro Virtual Docker Batchjob Finished Batchjob started to 31 aug 09 07 45 2006 Elapsed 00 01 48 Finish i 09 11 37 Remaining 00 02 03 ame l Working path C Program Files Molegro MVD2006 DockingOutput Current ligand 1 1runs Waaa asana nannan nani 100 Log Poses current ligand 2 Poses all 2 Graph 956 26 576 03 0 0 1000 0 Blue Energy of best pose Red Mean Energy of candidate population Res
84. job dialog will pop up showing the current status and progress of the docking see Figures 52 and 57 molegro virtual docker user manual 5 Docking Functionality page 62 129 E Molegro Virtual Docker Batchjob Running Batchjob started to 4 maj 10 46 28 2006 Elapsed 00 00 13 Finish estimated 10 50 58 Remaining 00 03 45 Working path c Program Files Molegro MVD2006 ScriptOutput Current ligand 1 1runs 8 Log Poses current ligand Poses all Graph Time De 10 46 29 304 Found grid in workspace 10 46 29 304 Setting evaluator init string cropdistance 0 hbond90 true 10 46 29 304 Setting optimizer init string cavity truepopsize 50 scalingfactor 0 50 crossoverrate 0 9 10 46 29 314 The random seed used for this session is 1710097600 10 46 29 314 Optimizer PopSize 50 ScaleF 0 5 PC 0 9 OffStretegy 1 earyTerm 0 01 SW 0 ForceCa 10 46 29 314 Evaluator TorsionScheme 1 dampFactor 1 cropDistance 0 useEPenal useE Intra 10 46 29 314 Creating Docking Results file c Program Files Molegro MVD2006 ScriptOutput Docki 10 46 29 344 Docking ligand XK2_263 10 46 29 374 Beginning run 1 out of 1 10 46 29 384 Source Ligand was randomized This will destroy its original orientation 10 46 34 151 Paused script 10 47 06 237 Resumed script 10 47 06 357 Evaluations s 55 0888 Accumulated 2039 Status Running Stop batchjob Figure 52 Docking Progress dialog
85. kspace Explorer see Figure 7 molegro virtual docker user manual 2 Docking Tutorial page 13 129 Workspace Explorer Create Surface Create Backbone Create Labels Detect Cavities Prepare All Proteins 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 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 III Cavity Prediction T o Figure 8 The predicted binding site molegro virtual docker user manual 2 Docking Tutorial page 14 129 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
86. le 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 overwrites existing filenames named lt filename pdb gt Examples DOWNLOAD 3ptb AS 3ptb pdb IMPORT All FROM 3ptb pdb DOCK 20 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 molegro virtual docker user manual 20 Appendix X Script Commands page 122 129 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 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 neste
87. lecule 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 A for distances less than 2 0 A Notice that although the electrostatic energy contribution has the theoretically predicted molegro virtual docker user manual 11 Appendix I Docking Scoring Function page 87 129 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 2 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 CH3 2 Lys N NHs 0 5 O atoms in COO Asp OD1 0D2 SOs Glu OE1 0E2 PO2 PO2 0 66 O atoms in PO 0 33 O atoms in SO3 1 0 N atoms in SO2NH Table 2 Charge templates Erp is a piecewise linear potential using two different sets of parameters One set for approximating the steric Van der
88. lecule names and residue atom IDs see Section 3 10 for more details The Workspace Explorer window see Figure 18 contains information about the 3D objects both molecules such as proteins ligands and structural waters but also objects such as labels surfaces backbones and cavities molegro virtual docker user manual 3 User Interface page 23 129 Workspace Explorer tems Options Workspace New v Fit to screen aC eee Ligands 1 Hide others E 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 4 Proteins 1 K KKE KK KK K K Figure 18 Workspace Explorer window The context menu right mouse button click allows the user to Export molecules to PDB Mol2 or SDF format Edit workspace properties Rename molecule Remove items from the current workspace Set the currently active ligand or reference ligand optional Copy ligands to poses used to inspect ligands with the Pose Organizer Clone ligand makes a copy of the ligand Convert ligand to pose or cofactor Convert protein to ligand Convert pose to ligand used when docking poses Modify ligand or pose using the Pose Modifier Detect cavities using the Cavity Prediction dialog Inspect poses using the Pose Organizer Prepare molecules Create labels surfaces and backbones Fit molecule to the visualization window
89. m Atom RMSD checking all automorphisms and Pairwise Atom Atom RMSD by molegro virtual docker user manual 6 Analyzing the Docking Results page 71 129 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 S RMSD Matrix Pairwise Atom Atom RMSD checking all automorphisms Name 0 1 2 8 0 XK2_263 0 579023 1 25688 1 30984 1 00 XK2_263 1 28563 1 32552 2 01 XK2_263 1 25688 1 28563 1 71806 3 02 XK2_263 1 30984 1 32552 1 71806 lt gt Molecule 1 00 XK2_263 Molecule 2 XK2_263 RMSD 0 579023 Copy to Clipboard Figure 58 RMSD Matrix dialog The dialog can be invoked by choosing RMSD Matrix from the Docking menu The Copy to Clipboard button can be used to copy the table to the clipboard for further inspection in an external text editor or spreadsheet 6 5 Structural Alignment Simple alignment of molecules is possible By selecting three atoms in one ligand and selecting three atoms in another ligand a new 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
90. molegro virtual docker page 2 129 Molegro ApS Copyright 2005 2006 Molegro ApS All rights reserved Molegro Virtual Docker MVD and MolDock are trademarks of Molegro ApS All the other trademarks mentioned within 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 Molegro ApS 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 Molegro ApS 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 3 129 Table of Contents 1 Introduction to Molegro Virtual Docker ssssssssssssrresssnrnnrsnrrrrsnnrrrs 5 I AMCONTACE Informatiesessie e N 6 1 2 System REC UIRGIMMOMUS cisccanusdnatadssewedetaamaranneonemmndiaaead niecesnand saa 6 1 3 Reporting Program Errors oc2x ccocesadesedechedndencase vos atenaeseeduceadacacess 6 1 4 Text Formats Used in the Manual ccceceeeeceee eee eeeeeeeeeeeeeaees 7 1 5 Screenshots Used In the ManW All icc icpecceusecivenseeedveivskansdewees vanities 7 1 6 Future UpdateS ssssasrsssssransrsnnnrssnnnrssannnssnnnnosnananrnunnrrsaanns 7 2 DOCKING TUtOMAliesn
91. n them will be shown in the Properties 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 35 129 Point Annotation a g Distance 2 47 A Torsion 4 19 b CE Angle 26 89 Selection Deselect All Set Selection as Center of Search Space Set Selection as Center of Distance Constraint Create Distance Annotation So 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 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 Window Labels menus molegro virtual docker user manual 3 User Interface page 36 129 Create Label Templa
92. ndomly 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 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 1 Notice an easy way to generate a Suitable initstring is to use the Docking Wizard to generate and save a generated script Clears the current workspace All molecules are removed from the workspace molegro virtual docker user manual 20 Appendix X Script Commands page 118 129 DOCKSETTTINGS lt initstring gt Determines the behavior of the docking engine The settings string is composed of semi colon
93. 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 10 for more details Finally 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 MVD2006 bin mvd currentPath The energy terms and their weights coefficients used in the ranking 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 ranking 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 8 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 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 General
94. ntial 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 MolDock Score fitness function 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 differential evolution may use a cavity prediction algorithm introduced in Appendix III 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 th
95. ntroduction to Molegro Virtual Docker Molegro Virtual Docker MVD is a program for determining the most likely conformation of how a ligand will bind to a macromolecule 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 introduction Chapter 1 Go through the docking tutorial Chapter 2 Read the instructions on how to use the GUI Chapter 3 a Read about Obtaining the Best Docking Results Chapter 8 Overall Chapters 3 to 9 describe various aspects of MVD from importing and preparing molecules to docking and inspecting the docked solutions Chapter 10 provides an overview of the new scripting features available from MVD v1 1 0 More detailed information about the algorithms cavity detection clustering binding mode prediction and scoring functions MolDock Score and MolDock Score Grid used by MVD can be found in the appendices molegro virtual docker user manual 1 Introduc
96. onsidered a technology preview version 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 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 molegro virtual docker user manual 21 Appendix XI MolDock SE page 125 129 into the initial population for the simplex evolution algorithm 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
97. ort 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 bugs molegro com Additionally Molegro Virtual Docker uses its own MVDML file format MVDML is a shorthand notation for Mo legro Virtual Docker Markup Language and is an molegro virtual docker user manual 15 Appendix V Supported File Formats page 97 129 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 a Search space center and radius a State information workspace properties Notice Currently the MVDML file format does not include cavities Also purely graphical objects e g labels interactions annotations backbones and surfaces are not saved molegro virtual docker user manual 16 Appendix VI Automatic Preparation The principles behind automatic preparation in MVD are described below a All rings closed loops are identified These rings are weeded out until a smallest subset capable of cov
98. ows the user to perform the necessary 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 molegro virtual docker user manual 4 Preparation page 44 129 Prepare Molecules f Missing Assign bonds f Missing Assign bond orders and hybridization f Missing Create explicit hydrogens F Miss 7 Assign charges EMi Detect flexible torsions in ligands fM Figure 38 Preparing molecules Within all preparation types the following four different possibilities are available see Figure 38 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 for bond orders all bonds are set to be single bonds for explicit hydrogens all hydrogens are removed 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
99. posed of a central 3D view referred to as the Visualization Window or 3D world together with a number of dockable windows introduced below 121p MVDML MVD2006 Eile dit View Rendering Preparation Docking Window Help C 2 a a g ea amp D a a Visualization Window e A a Partial charge 0 5 Hybridization Ter ue 0 Average an Q Console Wincow Figure 16 Main application window molegro virtual docker user manual 3 User Interface page 22 129 The MVD Toolbar provides easy and fast access to commonly used actions such as import of molecules docking using the Docking Wizard and pose inspection using the Pose Organizer Docking Wizard Label Dialog Screen Capture Undo Redo Toggle Fog Hide Distant VT PS G j y Q ig amp X Hydrogens Fog Hide Residues Search v Pose Organizer Online Help Toggle Hydrogen Workspace Finder Views Import Molecules Fit to Screen Figure 17 MVD Toolbar The MVD Toolbar also contains three 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 more details The Workspace Finder located at the far right side of the toolbar can be used to quickly search for mo
100. poses obtained from different ligands the Only show top option can be used focus on the most promising poses for each ligand The selection of the top poses are based on the currently chosen Sorting criteria Pose Organizer File Edit Table Settings Poses Name Ligand MolScore Affinity Rerank Score HBond 00 XK2 XK2_263 242 796 30 6705 186 316 15 5613 01 XK2 XK2_263 203 952 29 7885 131 966 13 0617 _ Dynamic update notice disables multiple poses selection C Only showtop 1 poses for each ligand Sorting criteria 1st MolScore 2nd None Pressing OK will keep 3 poses Figure 54 The Pose Organizer dialog Notice A detailed energy analysis is available by right clicking poses in the table and selecting Show Detailed Energy Analysis 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 6 Analyzing the Docking Results page 66 129 The Settings Tab Pane of the Pose Organizer can be used to customize the Pose Organizer see Figure 55 Pose Organizer C Orient hydrogens to optimal position C Show electrostatic interactions _ Display only residues close to ligand slow Re evaluation of poses Ranking Score coefficients misc data RerankingCoefficients bt
101. r abbreviation HIS CYS LETTER 1 letter abbreviation molegro virtual docker user manual 20 Appendix X 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 20 Appendix X Script Commands page 111 129 20 1 List of Script Commands Available Comments in MVD script files 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 s
102. r solid polygons Create Surface H LJ Cofactors 2 Proteins 2 a Poses 1 O Ligands 1 Surface type coloring Electrostatic v Figure 31 Creating a new surface Surfaces can be created via Create Surface from the context menu in the Workspace Explorer or via Window Surfaces molegro virtual docker user manual 3 User Interface page 38 129 lt Create Surface Drawing style Transparency Choose color Figure 32 Changing surface appearance 3 16 Creating Protein Backbones The backbone of the protein can be visualized by using the Create Backbone dialog The dialog can be invoked by using the context menu on the Proteins category or a single Protein item in the Workspace Explorer Create Backbone Backbone Target THVR Al 520 atoms 1HVR B 920 atoms Graphics style Cartoon Color scheme Color by structure Color interpolation Diameter A 0 30 4 Subdivisions 8 v J Figure 33 Creating a new backbone molegro virtual docker user manual 3 User Interface page 39 129 The Create Backbone dialog allows you to select which proteins or protein chains the backbone should be created for Two main graphics styles can be used The Cartoon style visualizes the secondary structure of the protein s using arrows to represent beta sheets and helical lines for alpha helices see Figur
103. 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 new search algorithm choose Search algorithm gt Algorithm gt MolDock SE experimental from the Docking Wizard The following parameters can be set 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 leas
104. rd Scoring Function gt Score gt MolDock Score GRID molegro virtual docker user manual 22 Appendix XII MolDock Score Grid page 128 129 Usage When Scripting 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 X Script Commands for more details molegro virtual docker user manual 23 Appendix XIII 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 Evolutionary 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
105. 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 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 7 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 a 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 5 1 Found cavities can be used to specify the origin of the search space in the Docking 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 import
106. ritten in bold face with initial capital letters Examples Workspace Explorer Macro Definition Ctrl O a 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 MVD2006 bin mvd exe 1 5 Screenshots Used In the Manual The screenshots used in the manual are taken from the Windows XP version of MVD Therefore dialogs and other GUI related material may slightly differ on other supported OS platforms e g Linux and Mac 1 6 Future Updates 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 6 New Version Found Latest version available 2006 1 0 3 Your current version 2006 1 0 0 Changes April 7th 2006 MVD 2006 Version 1 0 3 Bugfixes and some new features See the Release Notes in the Molegro Customer Area for a full list of changes March 20th 2006 MVD 2006 Version 1 0 2 Bugfixes and some new features See the Release Notes in the Molegro Customer Area for a full list of changes v J Anew version has been found Please go to www_molegro com to update
107. rue false Determines whether ligand self interaction energy should be taken into account 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 O the default settings the size of the active search space is used Other 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 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 water true false Determines whether water should be taken into account In addition to these parameters the following parameter option is available when using the Grid based scoring function gridresolution double Sets the grid spacing where the grid resolution is specified in Angstrom molegro virtual docker user manual 20 Appendix X Script Commands page 115 129 EVALUATOR lt initstring gt The default settings from the docking wizard will generate the following evaluator string EVALUATOR
108. 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 molegro virtual docker user manual 4 Preparation page 47 129 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 4 4 Pro
109. 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 1 MaxPoses Determines the maximum number of poses returned by the clustering described above Default value is 5 The default settings corresponds to the following script command DOCKSETTINGS maxIterations 2000 runs 1 ignoreSimilarPoses true IgnoreSimilarPosesThreshold 1 0 MaxPoses 5 It is not necessary to specify all of the parameters If only some of them are specified the default parameters will be 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 molegro virtual docker user manual 20 Appendix
110. srrsssnrrrssrrrrnrrnnnnrssnnrrssnnrrssnnnan 71 7 Customizing Molegro Virtual Docker sssssssssrrsrrssnrrsrrrsnrrnsrrrnnene 72 7 1 General PreferenceS ssssssrrssrrrnrrrnnrrrrrrnrrrenrrsnrrrsrrrnrrrnn 72 7 2 Command Line Parameters cscs sccteevenieed veces cen See tectesseneeeadecoreaans 74 7 3 Changing Ranking Score Coefficients ccccccceeeeeeeeeeeeeeeeeaeees 75 8 Obtaining the Best Docking ReSUItS cccceeceeeee eee ee teense eee eneeee ees 76 8 1 PRE Palau tnccanes se segeak da nenses e E a EEE iss 76 8 2 TO OCI Millet oa2 ain ee team tadcmetmenisaaanencn eee bananaceiesataaversenosaaneacaceamats 77 8 3 POSHOANAYSSisctrincithedniarequindanin Hagoniihines antigen niatiaeeboniesinaadusls 78 9 MUD siesta sera ind ceca e e sodgerans E tested wun E E 79 9 LOnline Hesienceiccntsecaetetssauidescaeeptansactessonstadaseseseseuservestentis 79 9 2 Tip of the Day ssssssssssssnnsrsnrrrrnrsrrrnssnnnrnesnnrrssnrrrnennrnrrnnnanrnne 80 9 3 The Molegro Website sssssasrsssssrunsnsnnnnnsnnnrssannnnsannnssnnnnenns 80 9 4 Technical SUpport ssssssssssssssrrsaarrrsaannnsnnnnnsrnnnnrrsaanrnsannnnennn 80 10 Script INGGM ACC iewet cosas truupiasivdevseeucieneseivnnised ie r a aai 81 10 1 Using the Script Interface ccc ccccccccseeenseeeeeessaeeeesseeeeeeeanes 81 10 2 Running a Text file SCrPliniws scscereonersaersesgurswaienrsteenerdiaeseeiaes 81 10 3 Examples of Common Script JObS s sssssssssrsssnrrrrsrrrrrersrrrssns 82
111. t lt lt Advanced settings Max number of ray checks Min number of ray hits Grid resolution 4 gt 4 gt 4 gt 4 gt gt Figure 41 Cavity Prediction dialog A dialog is available for detecting cavities see Figure 41 allowing to customize the sensibility and type of cavity search The Cavity Prediction molegro virtual docker user manual 5 Docking Functionality page 50 129 dialog can be invoked via the context menu in the Workspace Explorer in the Proteins category or by selecting the Detect Cavities menu option from the Preparation menu 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 Notice If no cavities are identified ligands can only bind to the surface of the protein or the cavity 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 l
112. t 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 molegro virtual docker user manual 21 Appendix XI MolDock SE page 126 129 Max Steps default 300 The number of iterations of the Nelder Mead simplex minimization procedure performed at each step of the MolDock SE algorithm Neighbour 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 X Script Commands for more details molegro virtual docker user manual 22 Appendix XII MolDock Score Grid MolDock Score
113. t 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 10 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 10 Script Interface page 83 129 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 X Script Commands ff Ine DOCKSETTINGS maxIterations 1000 runs 1 MaxPoses 5 EVALUATOR cropdistance 0 hbond90 true water tru OPTIMIZER cavity true popsize 50 crossoverrate 0 9 keepmaxposes 5 Dock LOAD 3PTB MVDML RMSD ligand 0 DOCK Docking Multiple Complexes Init DOCKSETTINGS maxIterations 1000 runs 1 MaxPoses 5 EVALUATOR cropdistance 0 hbond90 true water tru OPTIMIZER cavity true popsize 50 crossoverrate 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
114. t hydrogen bond directionality is not taken into account The grid based scoring function provides a 4 5 times speed up by precalculating potential energy values on an evenly spaced cubic grid see Appendix Appendix XII MolDock Score Grid for more details Docking Wizard Choose Scoring Function and Define Binding Site Scoring function Score MolDock Score Ignore distant atoms Enforce hydrogen bond directionality Binding site Origin User defined Center 60 3 05 Radius 5 E Cancel Figure 45 Choosing scoring function The Ignore distant atoms option is used to ignore atoms far away from 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 For the grid based scoring function the Grid resolution option not shown in Figure
115. tains settings related to the Visualization Window 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 Preferences General Graphics Debug C Show pivot point rotational center E Show root atom _ Fade 3D labels when in background Quality 5 Reset All to Defaults H Apply i Figure 60 The graphics tab of the Preferences dialog The final settings tab Debug contains various options that can be used to provide additional debug information molegro virtual docker user manual 7 Customizing Molegro Virtual Docker page 74 129 Preferences General Graphics Debug Create system log in Logs directory E Show population while docking C Show bounding boxes Use vector angle representation for poses C Extended GUI debug prop
116. tc acenessueseriensrquened a AEE OEE AN EEEE 8 2 1 Importing and Preparing MoleculeS sssssssssrrsssrrrrnrrrrrnrsrrresss 8 2 2 Running the Docking Simulation ssssssssssssrrsnrrsrnrssrrrsrrrnrnns 14 2 3 Viewing the ResultS ssssssssssssrsssnrrsssnrrrnrnrrenrnnnnrrnnnnresnnnrre 18 3 User Inte ACS ainai ipaa AEAT A A ARa iT ER 21 Bak OVEIVIGW irine ieie erna a ina N e A E a 21 3 2 BO Metre ce s eects alas rors a tie ae sie wean seer a EEE ETETEA 22 3 3 Workspace EXPO he lisistis te iiusavids eres sy nseiunnedistyietenriieeiatonds 22 3 4 Properties WINKOW ccccccceensescceeeeeeennneseseeeeeeeennnsasaeaeseeeenes 24 3 5 Visualization WINGDGWssssccatsececadusseaseeiedadsabcionddietaseubsedddeaxccececs 25 3 6 Console WINDOW saaisinsatrtines dated bhicswbincaee diane sbacedanseaebadaactesiadeind 28 3 7 Macro and Menu ECIGl cisisicsceasdendes einen ka iwaivtewsadeonusnvenmeeetantis 29 3 8 Clipping PlaneS ssssassssssssassssnarrsusnrrnannnnsnnnnnonnnnnnnsnnnrrsaanan 30 3 9 Hiding Distant ResidUeS ssssssssrrsasrrnsnsnnnsnsnanrssaanrnsnnnnnennn 31 3 10 Workspace Finder sssssssssrsssssrrnnssnnrrssnrrrrnnnnrrnnnnrrensnrnnnns 32 3 11 SEQUENCE VIEW Clic viwarvsesnesivaddsnatwcivienetseiuadetaawreeiaiiieneedawsied 33 3 12 Workspace PropertieS s sssssssssnrrrsnnrrrnrsnrnnsnnnnrrsnnnrrsnnnrns 34 3 13 Measurements and AnnotationS sssssssssssssrrrsssnrrresrrrrrrnrna 34 3 14 Creating LAE Siti tssauacat ovis ada
117. te Index Te T Cofactors 2 OR O Poses 1 Ligands 1 oe Figure 29 Creating a new label The Create Label dialog makes it possible to label different object levels atoms bonds molecules residues or torsion trees The labels can be chosen from a list of standard templates or constructed from a list of available variables using the Advanced tab Create Label Label Type Atom Template Index Target s O Cofactors 2 Label Expression a O BSS D w O Poses 1 E Ligands 1 Enter label expression in the combobox above Variable names will be substituted when evaluated Variables can be insert from the list below Variables ELE Element number Etot Total energy FC Formal Charge HBOND Hbond Acceptor donor e Inset in Label Expression Figure 30 Advanced label expression dialog molegro virtual docker user manual 3 User Interface page 37 129 Labels will occur in the Labels category in the Workspace Explorer and can be removed or hidden using the context menu or by pressing the labels tool bar button 3 15 Creating Molecular Surfaces Surfaces can be created for all molecular objects and subsequently customized Support for Solvent or Surface Accessible Surfaces coloring by Hydrophobicity Electrostatic Potential or Solid Color Surfaces can be drawn transparently as dots lines o
118. the Contents tab It is also possible to perform a full text search by choosing the Search tab from the sidebar 9 2 Tip of the Day A Tip of the Day dialog see Figure 63 providing useful tips on how to use Molegro Virtual Docker is available Tip of the Day D Did you know Quick inspection of molecules An easy way to browse the structures in the current workspace is by using the Workspace Explorer together with keyboard modifiers Selecting a molecule while holding SHIFT will zoom to the molecule Selecting a ligand while holding SHIFT CTRL SHIFT COMMAND on Mac will zoom to the molecule and display its hydrogen bond interactions with the protein Figure 63 Tip of the Day dialog 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 9 3 The Molegro Website The Molegro website also offers certain help facilities Please visit www molegro com to see our FAQ s and other information available 9 4 Technical Support Technical support is available for commercial licenses industrial and academic only To obtain additional support send an email to support molegro com molegro virtual docker user manual 10 Script Interface The default behavior for docking molecules in Molegro Virtual Docker is to start the application load and prepare the molecules
119. ties 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 molegro virtual docker user manual 3 User Interface page 25 129 Property Value Selection Position 2 164 8 951 26 069 Residue GLY 52 Intemal residue ID 51 Atom ID 458 Element C 6 PDB atom name CA Implicit hydrogens 0 VdW radius 174 Covalent radius 0 68 A Hydrogen bonding Nonpolar Partial charge 0 Hybridization Sp3 Temperature 42 34 Average angle 112 039 Clear Selection Figure 19 Example of properties for a selected atom visualiza The Visualization Window see Figure 20 visualizes all the selected molecules in the workspace and various objects to highlight import aspects e g labels annotations charges protonation guides backbones and surfaces Moreover cavities are visualized to allow for easy inspection of potential binding sites 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 transparent 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 visualizat
120. tion to Molegro Virtual Docker page 6 129 Molegro Virtual Docker is developed by Molegro ApS Hgegh Guldbergs Gade 10 Building 1090 DK 8000 Aarhus C Denmark www molegro com Information a Phone 45 8942 3165 a Fax 45 8942 3077 a VAT no DK 2832 6947 E mail General inquiries info molegro com Product support support molegro com a Reporting bugs bugs molegro com The system requirements for Molegro Virtual Docker are Windows 2000 XP or 2003 a Linux Most standard distributions such as Fedora Core 3 or later versions and Red Hat Please send a mail to support molegro com if the program does not work on a particular distribution and we will try to provide a new build a Mac OS X 10 3 9 or later versions a Please contact us for information about running MVD on other operating systems If you discover a program error please mail the information to bugs molegro 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 7 129 1 4 Text Formats Used in the Manual The following formatting styles are used in this manual a All GUI text labels and keyboard shortcuts are w
121. tonation Wizard This wizard highlights residues likely to have a non standard protonation state such as histidine and makes it easy to change the protonation state via the context menu To invoke the wizard choose Preparation Protonation Wizard Protonation Wizard Display guides for the following residues l GLU Only display residues close to active ligand C Show residue charges Show labels Auto Protonate Based on Explicit Hydrogens Auto Protonate To Default Protonation States Residue list Protein ID Residue Protonation Details ASP 128 ASP Default GLU 44 GLU Default GLU51 GLU Default HIS 87 HID Default ND1 Protonated HIS 127 HID Default ND1 Protonated In order to manually protonate residues use the context menu on the residues guides yellow spheres in the 3D world Figure 39 Protonation Wizard The top panel Display guides for the following residues chooses which residues to display in the 3D view molegro virtual docker user manual 4 Preparation page 48 129 The Options panel can be used to toggle whether only residues close to the active ligand should be displayed and whether charges and labels should be displayed or not Two buttons make it possible to perform automatic protonation The first Auto Protonate Based on Explicit Hydrogens can be used if the protein has been prepared in another program and the hydrogens have been explicitly set This method will ass
122. ults p s Molegro MVD2006 DockingOutput DockingResuits mvdresults 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 Because 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 MVD2006 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 2 Dragging and dropping the DockingResults mvdresults file onto the MVD application 3 Dragging and dropping the DockingResults icon E onto the MVD application molegro virtual docker user manual 2 Docking Tutorial page 18 129 The DockingResults mvdresults file is located in the Output directory together with a docking log file and the poses found in SDF file format After importing the DockingResults mvdresults file the Pose Organizer will appear showing the poses found see Figure 13
123. ure Docking Wizard Customize Search Algorithm Search algorithm Algorithm MolDock Optimizer Number of runs 15 Randomize ligand orientation onstrain poses to cavity no cavities foun Parameter settings Population size 50 Max iterations 2000 Scaling factor 10 50 Crossover rate 0 90 Offspring scheme Scheme 1 S S 85 85 85 Termination scheme Variance based Cancel Figure 48 Customizing the search algorithm Pose Clustering 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 molegro virtual docker user manual 5 Docking Functionality page 59 129 docking run and only the most promising ones will be reported Several options are available a 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 IV Clustering Algorithm
124. 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 Figure 9 Selecting the binding site 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 number 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 5 3 Finally the Output directory specifies where the docking data log file and found poses w
125. zed 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 either the Ranking Score or the Binding Affinity estimate The Ranking Score makes use of a more advanced scoring scheme than the docking scoring function used during the docking run Using the Ranking Score will often increase the accuracy of the ranked order of the poses molegro virtual docker user manual 9 Help 9 1 Online Help E Molegro Virtual Docker MVD Help File Edit View Go Bookmarks Help esI 095 AA vY VBBUBBBUD Sidebar x Sidebar x B MVD Help Contents Index Bookmarks Search pee gt Molegro Virtual Docker 2006 in Introduction to Molegro Virtual Docker O Docking Tutorial t U User Interface U Preparation t U Docking Functionality U Customizing Molegro Virtual Docker oO Help E U Aprendices U Glossary Welcome to the MVD Online Help System Choose a manual section from the menu to the left Figure 62 Screenshot from the online help system The documentation for Molegro Virtual Docker is available both as indexed online help HTML formatted and as a PDF file In order to invoke the online help choose Help MVD Help from the menu bar molegro virtual docker user manual 9 Help page 80 129 In the sidebar you can browse the different chapters in

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