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Cocrystallized ligand redocking 1-2

Cocrystallized Ligand Redocking

Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized ligands are rescored with Glide or Prime mm-gb/sa or redocked and the corresponding RMSD is measured.

This workflow is derived from the work published by Paulette Greenidge from Novartis in:
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Sherman, W.; J. Chem. Inf. Model. 2014, 54(10), 2697–717

MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Wolf, R.M.; J. Chem. Inf. Model. 2013, 53(1), 201–9

[Requires: Glide, LigPrep, Prime]

Cocrystallized Ligand Redocking: Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized ligands are rescored with Glide or Prime mm-gb/sa or redocked and the corresponding RMSD is measured. This workflow is derived from the work published by Paulette Greenidge from Novartis in:Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Sherman, W.; J. Chem. Inf. Model. 2014, 54(10), 2697–717MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Wolf, R.M.; J. Chem. Inf. Model. 2013, 53(1), 201–9[Requires: Glide, LigPrep, Prime] 856 PDBprotein-ligand complexes10 first One protein-ligand complex Ligands ASL = ligand centroidAround the detected ligandRedocking poses inspectionLigandsRedockingRMSD x ray pose first No minimizationCheck the Ligand detection settings in Maestro Preferences IterationRemoveinitial Ligand detection checkeg PPI PROPANOIC ACIDjoin indexUnique concatenateAs SMILES Preprocess(incl. bond order)-merge_ligands_with_chain-merge_waters_with_chainm.atoms 5-130 Smallest ligand and the corresponding chainLigands and cofactorsLigands ASL = ligandChains with small molecules mergedLigand sizePID ID, #atomsAnd other ligands/cofactors LigandsASL = ligand AND NOT <cofactor list> cocrystallized ligand preparationcrystallized ligand redockingMinimization failuresView problemsfor structures to fix manuallycentroidAround the ligandFailuresLogView problemsfor structures (use Find functionality)PDB classification Rescoring Rescoring LigandsPDB set SMILES patternTable Creator Row Splitter RMSD Get PDB ParallelChunk Start Parallel Chunk End Get PDB Split by Structure Table Row to Variable(deprecated) Chunk Loop Start Column Filter Glide GridGeneration Glide Grid Writer Run Maestro Row Filter Table Viewer Concatenate Run Maestro Command Protein PreparationWizard KNIME-MaestroConnector Joiner Math Formula Column Filter Extract Atom/bondProperties Table Viewer Math Formula GroupBy String-to-Type Loop End Protein PreparationWizard Java Edit Variable Column Rename GroupBy MAE-to-Smiles Split by Structure Split by Structure Sorter Extract Properties Row Splitter Column Resorter Preprocess andsplit by chain Ligand detection Table Row to Variable(deprecated) Ligand detection Preprocess andsplit by chain Loop End Get PDB Chunk Loop Start Split by Structure LigPrep Glide LigandDocking Row Splitter Protein PreparationWizard Run Maestro Glide GridGeneration Glide Grid Writer Row Splitter Table Viewer Run Maestro Extract Properties Prime MM-GBSA Complexes-to-PoseViewers Ungroup MAE Table Viewer Column Filter Row Filter Table Viewer Column Resorter Cell Splitter Cocrystallized Ligand Redocking: Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized ligands are rescored with Glide or Prime mm-gb/sa or redocked and the corresponding RMSD is measured. This workflow is derived from the work published by Paulette Greenidge from Novartis in:Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Sherman, W.; J. Chem. Inf. Model. 2014, 54(10), 2697–717MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Wolf, R.M.; J. Chem. Inf. Model. 2013, 53(1), 201–9[Requires: Glide, LigPrep, Prime] 856 PDBprotein-ligand complexes10 first One protein-ligand complex Ligands ASL = ligand centroidAround the detected ligandRedocking poses inspectionLigandsRedockingRMSD x ray pose first No minimizationCheck the Ligand detection settings in Maestro Preferences IterationRemoveinitial Ligand detection checkeg PPI PROPANOIC ACIDjoin indexUnique concatenateAs SMILESPreprocess(incl. bond order)-merge_ligands_with_chain-merge_waters_with_chainm.atoms 5-130 Smallest ligand and the corresponding chainLigands and cofactorsLigands ASL = ligandChains with small molecules mergedLigand sizePID ID, #atomsAnd other ligands/cofactors LigandsASL = ligand AND NOT <cofactor list> cocrystallized ligand preparationcrystallized ligand redockingMinimization failuresView problemsfor structures to fix manuallycentroidAround the ligandFailuresLogView problemsfor structures (use Find functionality)PDB classification Rescoring Rescoring LigandsPDB set SMILES patternTable Creator Row Splitter RMSD Get PDB ParallelChunk Start Parallel Chunk End Get PDB Split by Structure Table Row to Variable(deprecated) Chunk Loop Start Column Filter Glide GridGeneration Glide Grid Writer Run Maestro Row Filter Table Viewer Concatenate Run Maestro Command Protein PreparationWizard KNIME-MaestroConnector Joiner Math Formula Column Filter Extract Atom/bondProperties Table Viewer Math Formula GroupBy String-to-Type Loop End Protein PreparationWizard Java Edit Variable Column Rename GroupBy MAE-to-Smiles Split by Structure Split by Structure Sorter Extract Properties Row Splitter Column Resorter Preprocess andsplit by chain Ligand detection Table Row to Variable(deprecated) Ligand detection Preprocess andsplit by chain Loop End Get PDB Chunk Loop Start Split by Structure LigPrep Glide LigandDocking Row Splitter Protein PreparationWizard Run Maestro Glide GridGeneration Glide Grid Writer Row Splitter Table Viewer Run Maestro Extract Properties Prime MM-GBSA Complexes-to-PoseViewers Ungroup MAE Table Viewer Column Filter Row Filter Table Viewer Column Resorter Cell Splitter

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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: jcmozzic
Created at: 2014-12-16
On NodePit since: 2020-08-12
Last update: 2024-11-18
Created with KNIME version: v4.3.2
Tags: Real WorldGlideLigPrepPrime

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