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Cocrystallized ligand redocking 1

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 Primemm-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] 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, #atomsRedockingRMSDcentroidLigandsOne protein-ligand complexRedocking poses inspectionAround the detected ligand No minimization And other ligands/cofactors x ray pose first cocrystallized ligand preparationcrystallized ligand redockingRun Maestro Command Protein PreparationWizard Java Edit Variable GroupBy MAE-to-Smiles Split by Structure Split by Structure Sorter Extract Properties Table Viewer Row Filter Get PDB Run Maestro Glide Grid Writer Glide GridGeneration RMSD Protein PreparationWizard Column Rename Column Filter Row Splitter Concatenate LigPrep Glide LigandDocking 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 Primemm-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] 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, #atomsRedockingRMSDcentroidLigandsOne protein-ligand complexRedocking poses inspectionAround the detected ligand No minimization And other ligands/cofactors x ray pose first cocrystallized ligand preparationcrystallized ligand redockingRun Maestro Command Protein PreparationWizard Java Edit Variable GroupBy MAE-to-Smiles Split by Structure Split by Structure Sorter Extract Properties Table Viewer Row Filter Get PDB Run Maestro Glide Grid Writer Glide GridGeneration RMSD Protein PreparationWizard Column Rename Column Filter Row Splitter Concatenate LigPrep Glide LigandDocking

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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: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: Real WorldGlideLigPrepPrime

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