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CCDC Running GOLD

CCDC Running GOLD

CCDC Running GOLD

This example workflow illustrates the use of the three GOLD-related components: CCDC GOLD Ligand Prep, CCDC GOLD Run Docking and CCDC GOLD Export Results.

CCDC Running GOLDThis example workflow illustrates the use of the three GOLD-related components: CCDC GOLD Ligand Prep, CCDC GOLD Run Docking and CCDC GOLD Export Results. Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive.The example target provided is Spleen Tyrosine Kinase (SYK) structure 5LMA, and the example ligands are compounds for which other SYK co-crystal structures areavailable or straightforward analogues thereof. The extra columns in the ligand CSV file are dummy data intended to illustrate that the data included are carried through thedocking process into the solution MOL2 files. The CCDC GOLD Run Docking component may also be used with arbitrary input ligands. In this case, ligands are read from anSDF file and are therefore in MOL format. Note that the ligand column is called 'Molecule' here and not 'gold_input' as it is above.Output is still in MOL2 format, even though thre input is in MOL format.Remember that, in this case, the user is responsible for ensuring ligands have been properly prepared. The CCDC GOLD Ligand Prep component takes SMILES input from its input table and generates high-quality 3D input structures in MOL2 format suitable for input into GOLD.Note that, at present, no (de)protonation, tautomer enumeration or stereocentre enumeration are performed. The CCDC GOLD Run Docking component takes an uploaded GOLD configuration file and 3D structures from a user-specified column and docks the input structures into thetarget specified in the configuration file. Hermes may optionally started once the docking run in finished so the full result set may be inspected. Output is in MOL2 format.Note that all configuration of the docking is performed via the pre-prepared GOLD conf file. Thus, to alter the docking (e.g. by using a different fitness function) the conf filemust be altered, either manually or by loading it into Hermes and using the GOLD menu therein.The CCDC GOLD Export Results component allows GOLD solutions in its input table to be exported as MOL2 files to a specified directory (which must exist and be empty). Allother columns are included as data items. Note that whatever solutions are in the table will be exported; this may thus be the full results set, or some filtering may have beenapplied. In addition, Hermes may optionally be started and will load the exported set. Read structuresas SMILESConvert SDF dataitems to columnsTrivial examplefiltering ofGOLD solutions CCDC GOLDLigand Prep CSV Reader SDF Reader SDF Extractor Filtering CCDC GOLDRun Docking CCDC GOLDExport Results CCDC GOLDRun Docking CCDC Running GOLDThis example workflow illustrates the use of the three GOLD-related components: CCDC GOLD Ligand Prep, CCDC GOLD Run Docking and CCDC GOLD Export Results. Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive.The example target provided is Spleen Tyrosine Kinase (SYK) structure 5LMA, and the example ligands are compounds for which other SYK co-crystal structures areavailable or straightforward analogues thereof. The extra columns in the ligand CSV file are dummy data intended to illustrate that the data included are carried through thedocking process into the solution MOL2 files. The CCDC GOLD Run Docking component may also be used with arbitrary input ligands. In this case, ligands are read from anSDF file and are therefore in MOL format. Note that the ligand column is called 'Molecule' here and not 'gold_input' as it is above.Output is still in MOL2 format, even though thre input is in MOL format.Remember that, in this case, the user is responsible for ensuring ligands have been properly prepared. The CCDC GOLD Ligand Prep component takes SMILES input from its input table and generates high-quality 3D input structures in MOL2 format suitable for input into GOLD.Note that, at present, no (de)protonation, tautomer enumeration or stereocentre enumeration are performed. The CCDC GOLD Run Docking component takes an uploaded GOLD configuration file and 3D structures from a user-specified column and docks the input structures into thetarget specified in the configuration file. Hermes may optionally started once the docking run in finished so the full result set may be inspected. Output is in MOL2 format.Note that all configuration of the docking is performed via the pre-prepared GOLD conf file. Thus, to alter the docking (e.g. by using a different fitness function) the conf filemust be altered, either manually or by loading it into Hermes and using the GOLD menu therein.The CCDC GOLD Export Results component allows GOLD solutions in its input table to be exported as MOL2 files to a specified directory (which must exist and be empty). Allother columns are included as data items. Note that whatever solutions are in the table will be exported; this may thus be the full results set, or some filtering may have beenapplied. In addition, Hermes may optionally be started and will load the exported set. Read structuresas SMILESConvert SDF dataitems to columnsTrivial examplefiltering ofGOLD solutions CCDC GOLDLigand Prep CSV Reader SDF Reader SDF Extractor Filtering CCDC GOLDRun Docking CCDC GOLDExport Results CCDC GOLDRun Docking

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: flatk
Created at: 2020-07-07
On NodePit since: 2020-09-10
Last update: 2024-04-26
Created with KNIME version: v4.1.3

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