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Raccoon v1.0 User Manual - Molecular Graphics Laboratory, TSRI

1. 7 AutoDock Raccoon AutoDock VS Preparation Tool Stefano Forli e The Scripps Research Institute szr r s Molecular Graphics Laboratory M nrersien 10550 N Torrey Pines Rd Q israr La Jolla California 92037 1000 USA November 12th 2009 v 1 1 1 Introduction 2 Installation 3 Quickstart Workstation Linux cluster 4 Interface description and usage 4 1 Toolbar menu 4 2 Ligands tab 4 3 Receptors tab 4 4 Maps tab 4 5 Docking tab 4 6 VS Generation 5 Results analysis 6 References 1 Introduction Raccoon is a graphical interface for processing ligand libraries in different formats PDB multi structure MOL2 and PDBQT multiple receptor conformations e g relaxed complex experiments and flexible residues to generate all the files required to run an AutoDock 1 virtual screening A basic knowledge of AutoDock and AutoDockTools is required The interface is composed of five tabs which encompass all the essential aspects that need to be addressed when preparing a virtual screening Ligand s Receptor s Maps Docking and VS Generation Although a few options require prior activation of at least a ligand and or a receptor the workflow is rather flexible so there is no predefined order to specifying required inputs for the VS generation The software automates some of the most common operations performed when preparing a virtual screening splitting multi structure fil
2. Add ligands Add a directory Browse where your ligands are and select files or directories 2 RECEPTOR S TAB Add the target structure by clicking on Add receptor file and navigate to the target structure file PDB PDBQT MOL2 3 MAPS TAB Add the GPF to be used in the VS by clicking Load a GPF template 4 DOCKING TAB From the pull down menu select docking setup pick the From template option then click on Generate default DPF OF Load DPF template 5 VS GENERATION TAB Specify the output directory where the virtual screening files will be generated by clicking on Set directory To create a new directory type the name in the file entry 6 VS GENERATION TAB Check that no red lines are left inside the Summary panel then press the GENERATE button and wait until the process is completed 7 RUN THE VIRTUAL SCREENING Lin Mac Win Cygwin To run the virtual screening open a terminal shell change directory to the location specified in the step 6 enter into the directory named after your target structure then launch the script RunVS sh Win Browse to the directory specified in step 6 then to the directory named after the target structure and double click on the file RunVS bat Raccoon quickstart PBS cluster GOAL Generate a virtual screening of ligand library on
3. Ee Hrilp Ugendps mecsptoris Mags Dochy WS Generation 4 Ampa target Mullipin nition ations Alera ii sinacturm Add receptor file Load the receptor structure MULTIPLE CONFORMATIONS MODE With Raccoon is possible to generate the files for a virtual screening of a set of ligands against multiple states of the same protein The target structures can be different snapshots of a molecular dynamics simulation 3 or an NMR ensemble The receptor structure can be loaded in any of the supported formats PDB MOL2 PDBQT Ligand and flexible residues PDBQT are automatically rejected Non PDBQT structures will be converted automatically using the PDBQT generation options Add a structure se mime target kiupie cnniowmatiars Load receptor structures in any of the Tp Ses supported formats Multiple selections can be made by pressing Ctrl and or Shift Add a directory It allows to load all the receptors in any of the supported formats contained in a directory Remove a structure and Remove All Ped a lou bre Arid a direcllur Meme a slan arne Aeniuese wll Remove a selected structure or the entire set respectively A good practice is to store the multiple target structures in a single directory Since an unique GPF template is going to be used all the structures must be aligned with the same reference structure and with the grid box defined in the GPF template Receptors option
4. Fita Iyara IEL Remove all Delete the entire ligand set Once one or more ligands are imported a check is performed before accepting them Target structures flexible residues incorrect PDBQTs and empty files are automatically excluded When more than one ligand is rejected user is asked whether inspect the list of problematic structures The File gt Load VS configuration or File gt Ilmport ligand list file menu entry can also be used to import ligands NOTE If the ligand structures were obtained as MOL2 from ZINC 2 Raccoon will save the single ligand structures using their ZINC ids making easy to track compounds Ligands options PDBQT GENERATION Any time a non PDBQT ligand is imported it will be automatically converted in PDBQT The options for the conversion are accessible via the PDBQT generation options button NOTE the options will affect newly imported ligands only PDB generation options Set defaults Restore the default values for all the options ESSERE Farlial changes Aid Gasteiger Keep onna I structura repair Partial charges Select whether to use the AutoDock Gasteiger charges or to keep the original charges in the molecule none bonds s hydrogens both Structure repair Perform a structure repair addin bonds and hydrogens Structure clean up nang b rr sr NONE non polar H lone pairs both Structure clean up Remove lone pairs an
5. 1 5 4 2 Edit the file raccoon bat if necessary to match your installation path set MGLPYTHONPATH C Program Files MGLTools 1 5 4 C Python25 python exe SMGLPYTHONPATH S raccoon py 3 Optional Create a link to raccoon bat on your desktop by dragging the icon of the file to the Desktop while pressing the Alt key 3 Quickstart Two quickstart guides follow which cover how to generate a simple virtual screening with a library of one or more ligands versus a single target receptor The first section presentes a quickstart guide for generating scripts for running a simple virtual screening on the local machine Linux Mac or Windows OS The second section covers generating scripts for running a simple virtual screening on a PBS cluster Linux OS More details on how to customize the virtual screening parameters are available on Section 4 Raccoon quickstart workstation GOAL Generate a virtual screening of ligand library on a single target structure Run the jobs on the local machine REQUIRED FILES Ligand structures one or more as PDB MOL2 or PDBQT files Receptor structure as PDB MOL2 or PDBQT file GPF generated by AutoDockTools centered and sized on the binding site optional DPF with the docking parameters to be used for all the ligands during the virtual screenings Step by step procedure 1 LIGAND S TAB Add one or more ligands by clicking on one of these buttons
6. a single target structure Run the jobs on a PBS cluster REQUIRED FILES Ligand structures one or more as PDB MOL2 or PDBQT files Receptor structure as PDB MOL2 or PDBQT file GPF generated by AutoDockTools centered and sized on the binding site optional DPF with the docking parameters to be used for all the ligands during the virtual screenings Step by step procedure 1 LIGAND S TAB Add one or more ligands by clicking on one of these buttons Add ligands Add a directory Browse to the location where ligands are stored and select files or directories 2 RECEPTOR S TAB Add the target structure by clicking on Add receptor file and navigate to the target structure file PDB PDBQT MOL2 3 MAPS TAB Add the GPF to be used in the VS by clicking Load a GPF template 4 DOCKING TAB From the pull down menu f select docking setup pick the From template option then click on Generate default DPF Of Load DPF template 5 VS GENERATION TAB Specify the output directory where the virtual screening files will be generated by clicking on Set directory To create a new directory type the name in the file entry 6 V8 GENERATION TAB Select the Linux cluster option in the OS options panel set the package generation options e g Tar file for shipping the files OPTIONAL change the CPU ti
7. bat Windows in each ligand directory for running single jobs independently This script contains the information to run AutoGrid if required and AutoDock NOTE Raccoon tries to guess the most suitable scripting format to be used based on the operating system on which it is executed On Unix like systems the scripts will be in Bash scripting language while on Windows the batch language will be used A special option Use Cygwin available on Windows systems sets the Bash language to be used in a Cygwin environment Create a VS package file After the generation process create a package containing all the files for the virtual screening to make easier to move the docking data on different machines The available formats are Tar Bz2 Gzip or uncompressed and Zip Linux cluster To generate the virtual screening files to be run on a cluster there are some extra options for defining the job submission to the queuing system CPU time per job This value defines the maximum amount of hours to use per ligand job before the calculation is killed The default OS Options is 24 hours This is a very conservative value but guarantees that the jobs have enough time to be completed The best value is different according to the calculation complexity and the cluster nodes speed Workstation Linux cluster scnpt generation master script for starting the Y5 Create a VS package file disabled Number of DLG s to run per ligand Accor
8. links save disk space 4 5 Docking tab A single set of parameters for the docking calculation is specified for the entire ligand set by using a template DPF when generating the parameters for each ligand Airra rian X aere kc ME Open a DPF Ele Help Docking parameters are generated for usenaca meceptaris maps Deck vs Generation each ligand by using a template DPF The DPF can be modified in place by pressing E EE IGNES the Edit button Recognized keywords meri at DEF mii MPF hendis will be represented with a bold font Generate default DPF Use this button to create a docking parameter file with the default AutoDock values The file can be customized with the Edit Save button Edit Save The DPF can be modified in place by pressing the Edit button and changes can be accepted with the Save button Raccoon parses the DPF and display recognized keywords colored in blue NOTE Raccoon doesn t check for the Welcome to te2coor ik aDczk Ys parameter file syntax so double check y ve M the file at any change ri AutoDock ut NOTE Raccoon only supports the use of LGA search algorithm Simulated annealing algorithm is not supported NOTE if a custom energy parameter file AD4 xxxx dat is defined in the DPF the user will be prompted to specify the file location The docking parameters should be selected to provide the best compromise between speed and accuracy and further
9. arameter file AD4 xxxx dat is defined in the GPF the user will be prompted to specify the file location If maps are already calculated never maps are already calculated option the map file manager is activated Pre e3foulaled naps Select the cached maps directory pia map dirertary defined yet Select the cached maps directory If maps have been already calculated the directory in which they are stored must be specified Once map directory is specified Raccoon will check for the presence of all atom types for the the current ligand set plus the desolvation and electrostatic special maps and their coherence same number of points center etc If all the checks pass the map files will be imported and used during the virtual screening generation CACHED MAPS On Unix like systems it is possible to use symbolic links to save disk space When cached maps now and cache the maps and never maps are already calculated options are used under Linux and Mac by default Raccoon will make symbolic links between the cached maps and the ligand directories When available this is the best choice for having the smallest hard disk footprint NOTE this option is not available on Windows due to the NTFS filesystem limitations Therefore the button is disabled on Windows Cached maps Two options are available Make copies use more disk space Make symbolic links save disk space Cached maps Make symbolic
10. d non polar hydrogens Activate special rotatable bonds yea no inacuvata ALL active Larktuge torsions Special rotatable bonds mido Specify types of bonds to be set as rotatable or kept rigid All the remaining guanidinium Fragmented structures standard rotatable bonds are set as rotatable by default Fragnenled 3s Qe gs s Keep largest fragment 4 Keep all gt Altach non bonded fragments Set the policy for managing problematic structures e g containing multiple fragments salts UK FILTER LIGAND LIST Specify a simple set of parameters to use to exclude ligands based on some of their structural properties hydrogen bond donors acceptors molecular weight number of atoms and rotatable bonds By default non AutoDock atom types are excluded NOTE Once the filters have been accepted they will be applied to current ligands as well as any subsequently loaded Filter presets Sets of predefined values in a pull down menu Ligand filters e Lipinski s rules except for the ClogP DrugLike Filer pres SET set DrugLike for fragments set The Default set provides the set of standard values within the Molecular properties AutoDock limits MIH MAX Preview For each criterion the Default button restores it to H bond donars fo 39 Defaut its initial value a fe ius CIN a EE Total number of ligands An estimate of the number of ligan
11. dingly to the available resources dockings of a CPU time per jah 74 00 00 et single ligand can be distributed among multiple nodes This value specifies how many nodes will run a single ligand job Therefore 100 poses per ligand can be generated either by setting the ga_run to 100 on the DPF and specifying 1 in the number of DLG s per ligand value or by reducing the ga_run to 10 and increasing the number of DLG s to run per ligand to 10 The results are a single DLG with 100 poses or 10 DLG s with 10 poses each respectively that can be clustered together using the summarize_results4 py script Humber of DLG s to run per ligand aet Generate button Once all the dependencies are satisfied so that all Summary entries are green the Generate button will be activated The first step is to write a log file in the virtual screening output directory containing all the information of the current virtual screening This log file can be used to re load data from a previous session and or replicate the calculations The log file format is raccoonVS YYYY MM DD log Raccoon generates a set of directories arranged accordingly to the following scheme single target multiple targets output directory output directory p J a raccoonvS Y Y MM DO log Poor receptor Runs sh bat maps ligand receptor ligand01_receptor ligand02 receptor ligand03_receptor re ey E raccoon S Y Y MM DD log 277 r
12. ds that will be Molecular weight 0 3933 Default Accepted ligands 0 accepted with any value set can be obtained reu Rejected ligands before being actually applied by pressing the Humber of atoms fo 393 Default Preview button at any time Rotatablebonds o 32 Defauit E Alter ligands with non AD atom types Rejected ligands will be highlighted in red in the ligand list Apply Rotatable bonds The maximum value for the rotatable bonds is set to that supported by AutoDock 32 When a flexible residue is loaded its rotatable bonds are included into the total count Therefore the maximum value allowed per ligand is reduced and ligands are filtered again 4 3 Receptors tab At the top of the Receptor s tab there are two buttons for selecting the options for switching between a classical virtual screening Single target on a single protein conformation and a docking versus an ensemble of protein states Multiple conformations Receptor structures can be imported in any of the supported formats PDB MOL2 PDBQT Ligand and flexible residues PDBQT are automatically rejected Non PDBQT structures will be automatically converted using the options specified in the PDBQT generation options panel SINGLE TARGET MODE The standard virtual screening approach docks a library of ligands onto a given target structure This mode requires the minimum input from the user a single structure file PEE Monee errs
13. e generated in a directory named Protease NCldiv NOTE even if the available disk space is measured and reported Raccoon doesn t perform any estimation of the space required for the generation 03 Oplurns Workstation x Fn rluster Script generation master script for starting the Y3 Create a v3 package file disabled Frr eprrr stri re Impnrter sure yy AutoDoc 7 OS options After preparing the files required by AutoDock for the docking calculations Raccoon can also be used to generate script files to automate the jobs executions on different systems Currently the two choices are Workstation to run the virtual screening on a single machine with any of AutoDock supported OS Linux Mac Solaris Windows or a Linux cluster NOTE the only cluster scheduler currently supported is PBS but the scripts should be easily adapted to run with different schedulers Workstation When generating the virtual screening for a workstation different options are available accordingly to the operating system Script generation master script for starting the VS generate a main script RunVS sh Linux Mac Solaris Win Cygwin or RunVS bat Windows A script is generated for each target and contains the information to run all the ligand jobs Unless special requirements are present this is the best choice single script for each ligand generate a script run sh Linux Mac Solaris Win Cygwin or run
14. eceptar01 RunV S sh bat gt maps ligand O receptori ligand 1 receptorQ1 ligand02 receptor 1 ligand0 3 receptor 1 re ee 77 receptor 2 RunV3 sh bat maps ligand00_receptor0z2 ligand 1 receptor02 ligand02_receptor02 ligand 3 receptor 2 TEETE 9 Results analysis When all the docking calculations are terminated the ligand poses need to be summarized and ranked so to proceed to inspect the most promising results Raccoon is designed to generate the files necessary to the virtual screening However currently it doesn t provide an interface for analyzing and filtering docked ligands Results analysis can be performed by using summarize_results4 py and other scripts in AutoDockTools This command can be invoked in a terminal using the following syntax Linux Mac pythonsh usr local mgltools i86Linux2 1 5 4 MGLToolsPckgs AutoDockTools Utilities24 summarize results4 py Win C Python25 python exe c Program Files MGLTools 1 5 4 MGLToolsPckgs AutoDockTools Utilities24 summarize results4 py The script usage is the following Usage summarize results4 py d directory Description of command q directory Optional parameters t rmsd tolerance default is 1 0 f rmsd reference filename default is to use input ligand coordinates from docking log b print best docking info only default is print all L print largest cluster info only default is print all B
15. es MOL2 generation of PDBQT input files ligand filter by number of atoms HB donor acceptors MW torsions generation of configuration files for both AutoGrid and AutoDock generation of scripts for running the virtual screening It supports use of pre calculated grid maps or can generate them on the fly during the generation phase Raccoon can be used to generate automatically all the scripts for running a virtual screening on the current machine or for submitting jobs on a Linux cluster PBS systems only The Virtual Screening Generation tab opens the Summary panel an overview of the current status It lists all the inputs yet to be defined colored in red When all requirements are satisfied the button for starting the generation is be activated A simple status bar is shown at the bottom of the interface Messages the end of any operations and potential errors are printed on the status bar Raccoon has been successfully tested on Linux Mac OS X and Windows 2K XP Vista HELP amp SUPPORT As for all the MGL software community and developers support for Raccoon is available through the Internet Any suggestions for improvements or bug reports are welcome Mailing list Subscribe to the AutoDock mailing list as described here http autodock scripps edu mailing list The best way to report a problem is to write a message with the prefix Raccoon in the subject and a short description of the issue Any error messages and fur
16. independently on separated machines DOLOS in each ligand job directory both GPF and DPF parameter files will be generated There is no need ETIN to have AutoGrid installed on the system on which Raccoon is running Lini Hera lure Mag Durkny MS GeT now and cache the maps AutoGrid will be executed just once during the generation phase by Raccoon including all the atom types found in the ligand set and map files will be cached Required map files will be copied or linked see Cached maps option in each ligand directory appropriately This option can be used 7 also with multiple receptors For this option it is 9 AutoDocK 7 necessary to have AutoGrid installed on the system on which Raccoon is running The software tries to guess the location of the AutoGrid binary autogrid4 for Linux and Mac autogrid4 exe for Windows If the binary is found its full path will be reported Otherwise a red button will be activated to manually specify the location If the binary is not defined the mode will be switched back to at each job NOTE this option is not available when AutoGrid is installed on Cygwin systems Change the Auth Grd exerutahle Cet the utoGrid executable Welscre 12 Flee pelnzckhezm fentropiahinautognd4 never maps are already calculated If AutoGrid calculation has already been performed or special custom maps are going to be used it is possible to specify the loca
17. me and number of DLG s 7 VS GENERATION TAB Check that no red lines are left inside the Summary panel then press the GENERATE button and wait until the process is completed 8 TERMINAL Either copy the VS directory or copy and un tar the package file if generated to the Linux cluster Move cd to the directory containing the virtual screening jobs and start the submission with vs submit sh 4 1 Toolbar menu The toolbar menu at the top of the window contains the functions relative to the current Raccoon session File File menu entry contains all the options for loading in and saving data from the current Raccoon session These include Load VS configuration Load a saved Raccoon session Once opened the file it is possible to select change 1 which dataset to load 2 the list of ligands 3 parameters for filtering the ligands 4 list of receptors 5 flexible residues 6 grid map settings 7 docking parameters and 8 virtual screening generation details By default all the options are selected Raccoon sessions are simple text files with a log extension They are automatically generated in the target directory when a virtual screening generation is performed Alternatively can be saved with the Save VS configuration entry in the File menu Save VS configuration Save the current Raccoon state The state can be saved at any moment allowing the user to resume a vir
18. print best docking and largest cluster info only default is print all o output filename default is summary or results a append to output filename default is to open output filename w build hydrogen bonds and report number built compute estat vdw hb desolv energies and report breakdown receptor filename report unbound energy subtract internal energy report depth of torsion tree verbose output Further information on how to use the scripts are available at the following link http autodock scripps edu faqs help how to how to summarize a directory of autodock4 docking results 6 References 1 Morris G M Huey R Lindstrom W Sanner M F Belew R K Goodsell D S Olson A J AutoDock4 and AutoDockTools4 Automated docking with selective receptor flexibility J Comput Chem 2009 30 16 2785 91 2 Irwin J J Shoichet B K ZINC a free database of commercially available compounds for virtual screening J Chem Inf Model 2005 45 1 177 82 3 Amaro R E R Baron J A McCammon An Improved Relaxed Complex Scheme for Receptor Flexibility in Computer Aided Drug Design J Comput Aided Mol Des 22 2008 693 705
19. s PDBQT GENERATION It contains all the available options for generating the PDBQT receptor structure from PDB or MOL2 Receptor PDBQT generation SE Set defaults Set defaults Restore the initial settings for all the options Partial charges Partial charges Set whether to use the AutoDock Gasteiger charges or to keep Add Gasteiger Keep original the original charges in the molecule Hem ve yes no Hon polar H gt Remove Lone pairs Define the clean up operations that will be performed on the receptor structure by selecting Water mol s 4 hd bd the features that will be removed during the PDBQT generation Hot standard res Altemate chains B 7 structure repair add H if missing OK Structure repair Perform a structure repair adding bonds and hydrogens NOTE All the options will affect the next imported receptor only FLEXIBLE RESIDUES PANEL It contains all the available options for importing or generating the flexible residues PDBQT file At least one target structure must have already been defined for this panel to be active From file Specify a flexible residue file generated with AutoDockTools through the Import PDBQT button Ligand PDBQT s will be rejected This choice is available on Single Target Mode only Jd Nesible resirues PDBGT generation options From selection Genera
20. structure MOL2 file and specify a directory in which to save the new single structure MOL2 files If the directory doesn t exist it will be created Help This menu contains the About command that can be used for identifying the current version of Raccoon 4 2 Ligands tab Raccoon supports the following ligand input formats PDB Protein Data Bank single or multiple structure MOL2 AutoDock formatted PDBQT The different file formats are managed automatically Whenever a multi structure MOL2 is detected the user will be asked to specify a directory to contain the resulting ligands At the end of the process the generated PDBQT files will be shown in the ligands list on the screen Duplicate files are automatically excludedand filtered using the current ligand filter set see Filter ligand list options Lis LHR Add ligands ipee Pea saint Linge TERR Eo It allows to load one or more ligands in any supported Ls pm ee See Rama kam formats Multiple selections can be performed by pressing Ctrl and or Shift keys peru Add a directory It allows to load all the ligands contained in selected directory JAdd recursively It allows to import all the ligands contained in the selected directory plus its sub directories Remove selected The ligands selected in the ligand list will be deleted from the set Use Shift and or Control for multiple selections PORGT yanaration npllne
21. te a flexible residues file by specifying one or more residue names using the following syntax THR276 threonine 276 B THR276 threonine 276 on chain B B THR276 B HIS229 threonine 276 and histidine 229 on chain B The syntax is case sensitive The presence of the selected residues will be checked in all the target structures before being accepted NOTE When flexible residues are either loaded from a file or defined from selection the maximum number of rotatable bonds acceptable for the ligands is correspondingly reduced to fit with the AutoDock limit of 32 maximum rotatable bonds When flexible residues are unset the standard value is restored Specifying flexible residues triggers re filtering ligands 4 4 Maps tab Use this tab to define all the options about the atomic maps to be used during the virtual screening Based on the operating system different options will be available AUTOGRID MODE Use the Run AutoGrid panel to specify when AutoGrid is executed for generating the interaction maps required by AutoDock at each job AutoGrid will run before any AutoDock job Tc oun U generating the required maps in each the ligand directory Using this options multiple copies of the em same maps will be created during the entire virtual M cnc M d screening This will require a large amount of disk space and is the most time consuming option This option is suitable for generating ligand jobs that can be run
22. ther details should be reported in the body of the email Forum Register for the MGL Forum by going here http mgl scripps edu forum Search for threads related to the issue encountered and if open a new thread if necessary 2 installation Raccoon requres the following software MGLTools v 1 5 4 or newer installed on your system although not essential installing AutoDock is strongly recommended for full access to all the features Go to http autodock scripps edu raccoon and download the files corresponding to your system Linux Mac 1 Extract all the content of the file raccoon tar gz in a directory i e your Desktop 2 Open a terminal cd to the directory where the file raccoon py has been extracted and type DVCHOHSII Xdccoon Dy If the pythonsh command is not recognized by the terminal specify the full path corresponding to your MGLTools installation for example Linux usr local mgltools i86Linux2 1 5 4 bin pythonsh raccoon py Mac Library MGLTools 1 5 4 bin pythonsh raccoon py 3 Optional Add an alias to your bashrc or cshrc for running Raccoon Bash alias raccoon usr local mgltools i86Linux2 1 5 4 bin pythonsh full path to raccoon py C shell alias raccoon usr local mgltools i86Linux2 1 5 4 bin pythonsh full path to raccoon py Windows 1 Extract all the files contained in the file raccoon win zip in the MGL Tools installation directory default C Program Files MGLTools
23. tion containing the map files For this option it is necessary to specify the directory containing the maps corresponding to the selected ligands For that reason this option requires that at least a ligand is present in the ligand set to be activated This option is not available in Multiple Conformation mode MAP FILES Accordingly to the selected AutoGrid mode different panels will be activated If maps files need to be calculated at each job and now and cache the maps options a GPF template panel is available HF template Load GPF template Lua GPF Laugikla nlusup frasconi T ES Tie belles wali parc rib If maps need to be calculated during the VS or DR NOUIS spacirmp 1 275 during the jobs preparation a template GPF m MM LE must be specified with this button liqand types LL K C A cep Mul mduldusgn xLDpulb Tidcenter 22 232 Bo tae 3 055 smo LEa C a p zut mini3r a mep p zMub e ll iga C ep p zut mend 3010 maS Edit Save p sul aliti ep mn p zxuut mzinis3c n0n ma The GPF can be modified in place by pressing p zMul aw013C2 22 ns T 2455 lecwap zwet miil EAI a mep the Edit button Changes can be saved with Bolwiap Hul mduz8J6 d may deleetric 3 1465 the Save button Raccoon parses the GPF and display recognized keywords colored in blue NOTE Raccoon doesn t guarantee check for the parameter file syntax so double check the file at any change NOTE if a custom energy p
24. tual screening setup later Import ligand list file Load a list of ligands to be included in the virtual screening The list is a text file that can be generated by any text editor or using the Export ligand list file option in the File menu The file must contain the complete path to the files to be loaded The file can include ligands in any supported format PDBQT MOL2 PDB Lines starting with will be ignored path to my pdbqt ligand000 pdbqt path to my pdbqt ligand001 pdbqt t path to my pdbqt ligand002 pdbqt path to my pdbqt ligand003 pdbqt path to my mo12 1001igands mol2 Each file will be processed according its format e g user will be prompted to split automatically multi structure MOL2 and filtered using the current filter set Duplicate files will be skipped Export ligand list file Save a list of ligands from the ligands currently loaded It is possible to choose whether to save ligands that have passed the filtering process or not or to chose to save the entire ligand set The ligand list can be loaded via the Import ligand list file menu option Utilities This menu contains optional useful functions present in Raccoon that can be used outside the virtual screening generation Split a MOL2 oplit a multi structure MOL2 file into single ligands The ZINC database 2 id is supported ligands with the ZINC id code in their name will be saved as ZINC id mol2 The user must select the multi
25. tuned for the complexity of the search number of torsions binding site size Moreover the amount of details output by AutoDock should be minimized by setting the outlev keyword in the DPF to O 4 6 VS Generation tab This tab contains the virtual screening generation summary and the operating system dependent options SUMMARY The status of the virtual screening generation can be accessed at any moment via the Summary panel Required input dependencies ligands receptors maps and docking parameters and the target directory where to generate the virtual screening files are displayed and colored accordingly to their status Incomplete and incomplete requirements are in colored in red and green respectively With the exception of a few correlated options the inputs for Raccoon can be specified in any order Whenever an operation is performed and all the requirements are met the corresponding dependency will be changed to green m Raccoon Autahoaock VS Ble uuites Help Liganu 5 Receplur s Mapes Duck vs Generar Set directory Specify the output directory in which the jobs will be SINE generated Liyanis 333223 accepted Although the software doesn t require any particular Recepior s 11 structures naming scheme the suggested format would be Maps none TargetName LigandSetName Therefore a virtual Ducking nur screening on a protease target with the NCI Diversity Bel direrinry Set would b

Raccoon v1.0 User Manual - Molecular Graphics Laboratory, TSRI

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