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MM Conformational search

Conformational search analysis

Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster representatives. Run the same analysis to compare two ConfGen modes.

[Requires: ConfGen] [Keywords: conformations, RMSD, distance, Python, rotatable bonds, analyze cocrystallized protein-ligand complexes, conformer clustering]

Conformational search analysis:Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster representatives. Runthe same analysis to compare two ConfGen modes.[Requires: ConfGen] [Keywords: conformations, RMSD, distance, Python, rotatable bonds, analyze cocrystallized protein-ligand complexes, conformer clustering] From Watts et al. "ConfGen: A Conformational Search Method for Efficient Generation ofBioactive Conformers" J. Chem. Inf. Model. 2010, 50, 534–546It could also be run on the other structures of the diverse ligand set from J. Chem. Inf. Model.2010, 534 :1cil,1ecv,1eou,1ftm,1g30,1pb9,1qbu,1qft,1s6p,1thm,1uyk,1vyz,1xor,1y1m,2a5t,2agt,2anj,2ath,2b55,2byi,2bz5,2c5o,2exm,2iqo,2izg,2pcp,2v3u,3cpa,3gwxDisabledin the conformersCocrystallized complexesLigands in 2DBest RMSD conformation Filter:rotatable bonds4-8RMSD calculation CombineReport creationOne or several protein-ligand complexesVisual inspectionScaffold to align the ligands: [N][C](=[N])[c]1[c][c][c][c][c]1Alignment on a scaffoldLowest RMSDLigands in 2DRMSD calculationLowest RMSDExtract the ligand(s)Post processing[activate the iinteractivity]Atom selectioneg 21 and 38Distance5 clusters Superimposed on the amidine1 formRepresentativeconformation Option in the node1 formExtract the ligand(s)DefaultsettingsDefaultsettingsWith minimizationTesting Table Viewer Get PDB Table Viewer Run Maestro Table Viewer Get PDB Ungroup MAE Run Maestro Run Maestro RMSD Table Viewer Table Viewer KNIME-MaestroConnector Table Row to Variable(deprecated) Conformer Cluster Run Maestro LigPrep Row Filter Ungroup MAE Extract Properties LigPrep ConfGen ConfGen ConfGen Conformational search analysis:Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster representatives. Runthe same analysis to compare two ConfGen modes.[Requires: ConfGen] [Keywords: conformations, RMSD, distance, Python, rotatable bonds, analyze cocrystallized protein-ligand complexes, conformer clustering] From Watts et al. "ConfGen: A Conformational Search Method for Efficient Generation ofBioactive Conformers" J. Chem. Inf. Model. 2010, 50, 534–546It could also be run on the other structures of the diverse ligand set from J. Chem. Inf. Model.2010, 534 :1cil,1ecv,1eou,1ftm,1g30,1pb9,1qbu,1qft,1s6p,1thm,1uyk,1vyz,1xor,1y1m,2a5t,2agt,2anj,2ath,2b55,2byi,2bz5,2c5o,2exm,2iqo,2izg,2pcp,2v3u,3cpa,3gwxDisabledin the conformersCocrystallized complexesLigands in 2DBest RMSD conformationFilter:rotatable bonds4-8RMSD calculation CombineReport creationOne or several protein-ligand complexesVisual inspectionScaffold to align the ligands: [N][C](=[N])[c]1[c][c][c][c][c]1Alignment on a scaffoldLowest RMSDLigands in 2DRMSD calculationLowest RMSDExtract the ligand(s)Post processing[activate the iinteractivity]Atom selectioneg 21 and 38Distance5 clusters Superimposed on the amidine1 formRepresentativeconformation Option in the node1 formExtract the ligand(s)DefaultsettingsDefaultsettingsWith minimizationTesting Table Viewer Get PDB Table Viewer Run Maestro Table Viewer Get PDB Ungroup MAE Run Maestro Run Maestro RMSD Table Viewer Table Viewer KNIME-MaestroConnector Table Row to Variable(deprecated) Conformer Cluster Run Maestro LigPrep Row Filter Ungroup MAE Extract Properties LigPrep ConfGen ConfGen ConfGen

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On NodePit since: 2020-11-12
Last update: 2026-01-22
Created with KNIME version: v4.1.3
Tags: Molecular mechanicsConfGenConfromationsRMSDDistancePythonRotatable BondsConformer Clustering

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