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MM Conformational search 1-3

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]in the conformersLigands in 2DOne or several protein-ligand complexesVisual inspectionScaffold to align the ligands: [N][C](=[N])[c]1[c][c][c][c][c]1Alignment on a scaffoldLowest RMSDLowest RMSDExtract the ligand(s)Post processing[interactive]Atom selectioneg 21 and 38Distance5 clusters Superimposed on the amidine%file%%file%1 formRepresentativeconformation Option in the nodeDefaultsettingsTable Viewer Table Viewer Get PDB Ungroup MAE Run Maestro Run Maestro RMSD Table Viewer KNIME-MaestroConnector Table Row to Variable(deprecated) Conformer Cluster Run Maestro Molecule Writer(from MAE) CSV Writer LigPrep Row Filter Ungroup MAE Extract Properties 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]in the conformersLigands in 2DOne or several protein-ligand complexesVisual inspectionScaffold to align the ligands: [N][C](=[N])[c]1[c][c][c][c][c]1Alignment on a scaffoldLowest RMSDLowest RMSDExtract the ligand(s)Post processing[interactive]Atom selectioneg 21 and 38Distance5 clusters Superimposed on the amidine%file%%file%1 formRepresentativeconformation Option in the nodeDefaultsettingsTable Viewer Table Viewer Get PDB Ungroup MAE Run Maestro Run Maestro RMSD Table Viewer KNIME-MaestroConnector Table Row to Variable(deprecated) Conformer Cluster Run Maestro Molecule Writer(from MAE) CSV Writer LigPrep Row Filter Ungroup MAE Extract Properties ConfGen

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On NodePit since: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: Molecular MechanicsConfGenConformationsRMSDDistancePythonRotatable BondsConformer Clustering

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