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Ligand alignment 1-2

Ligand alignment
Ligand alignment:Align a set of ligand structures flexibly with torsional variation, using a best practicesapproach to choose the most appropriate method. The ligands can be similar (acongeneric series, for example, or multiple congeneric series with different cores) ordiverse.Referenceligandconformation3 congeneric ligandsKNIME_batch.py Optionsutilities/align_ligandsOptionsGlobal flexible alignment(automatic)Runs align_ligandsAlignmenton a flexible reference(Sample reference ligand)Runs flex_alignAlignment on the largest Bernis-Murcko scaffoldof a rigid reference ligandRuns align_ligand -refAlignment on a section of a rigid reference liganddefined with a SMARTSRuns align_ligand -ref -coreAll ligandsand reference SMARTSAlignment on the Maximum Common Substructurewith a rigid reference ligandRuns align_ligand -ref -mcsVisual inspectionSee the LIgand alignment node Advanced sampling optionsto improve the alignmentVisual inspection(reference included)SimilaritySimilarityVisual inspection(reference included)Alignment on a section of a rigid reference liganddefined with a SMARTSfrom a variable3D coordinatesSimilarityVisual inspection(reference included)MCSin the set of ligandsutilities/flex_alignuses Shape_screentechnologyOptionsVisual inspection(reference included) Protection quotesVisual inspection(reference included)SimilarityDisabledMolecule Reader(to MAE) SDF Reader Get Help Table Viewer Get Help Table Viewer Ligand Alignment Ligand Alignment Ligand Alignment Ligand Alignment Maximum CommonSubstructure Search Concatenate Extract Properties Ligand Alignment Run Maestro Run Maestro Extract Properties Extract Properties Run Maestro Ligand Alignment LigPrep Extract Properties Run Maestro Run Maestro Get Help Table Viewer Run Maestro Table Rowto Variable String Manipulation(Variable) Run Maestro Extract Properties Config Testing Ligand alignment:Align a set of ligand structures flexibly with torsional variation, using a best practicesapproach to choose the most appropriate method. The ligands can be similar (acongeneric series, for example, or multiple congeneric series with different cores) ordiverse.Referenceligandconformation3 congeneric ligandsKNIME_batch.py Optionsutilities/align_ligandsOptionsGlobal flexible alignment(automatic)Runs align_ligandsAlignmenton a flexible reference(Sample reference ligand)Runs flex_alignAlignment on the largest Bernis-Murcko scaffoldof a rigid reference ligandRuns align_ligand -refAlignment on a section of a rigid reference liganddefined with a SMARTSRuns align_ligand -ref -coreAll ligandsand reference SMARTSAlignment on the Maximum Common Substructurewith a rigid reference ligandRuns align_ligand -ref -mcsVisual inspectionSee the LIgand alignment node Advanced sampling optionsto improve the alignmentVisual inspection(reference included)SimilaritySimilarityVisual inspection(reference included)Alignment on a section of a rigid reference liganddefined with a SMARTSfrom a variable3D coordinatesSimilarityVisual inspection(reference included)MCSin the set of ligandsutilities/flex_alignuses Shape_screentechnologyOptionsVisual inspection(reference included) Protection quotesVisual inspection(reference included)SimilarityDisabledMolecule Reader(to MAE) SDF Reader Get Help Table Viewer Get Help Table Viewer Ligand Alignment Ligand Alignment Ligand Alignment Ligand Alignment Maximum CommonSubstructure Search Concatenate Extract Properties Ligand Alignment Run Maestro Run Maestro Extract Properties Extract Properties Run Maestro Ligand Alignment LigPrep Extract Properties Run Maestro Run Maestro Get Help Table Viewer Run Maestro Table Rowto Variable String Manipulation(Variable) Run Maestro Extract Properties Config Testing

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Created by: jcmozzic
Created at: 2020-01-31
On NodePit since: 2021-05-19
Last update: 2024-12-17
Created with KNIME version: v4.3.2
Tags: LigPrep

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