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Low energy conformations

It runs a MacroModel or ConfGen conformational search on structures prepared with LigPrep. Optionally align them on a reference to inspect the conformational spaces in the context of the binding site.

[32162] 21.2.1
See details on https://kni.me/w/eAckV-NVB9b9o_rG

This workflow is uploaded as Computational model when executing the Upload model to LiveDesign node. The KNIME workflow can then be run in LiveDesign on the LiveReport structures. The output column(s) will be added to the LiveReport. Changelog:22.2.4 - Automatic protocol selection and installation21.2.1 - MacroModel structures are aligned as well21.2.0 - Control to generate several LigPrep forms Uses Primary_host and 1 CPU21.1.2 - Better pose naming21.1.1 - Alignment on a core section Energy difference in kcal/mol Lowest conformations from MacroModel20.4.1 - ConfGen branch Alignment on a reference specified in the admin page (file or corporate ID) Adapted to the energy column name change in 21-1 Parameter(s) which can be changed from the Admin page or the Parametrized model panel:- The LigPrep optionsIn quotes: eg -ligprepOptions "-s 4 -epik -pht 2". See $SCHRODINGER/ligprep -h message- The conformational search method (ConfGen of MacroModel)eg -ConfGen true- The number of conformers eg -max_num_conformers 10- The aligment reference or core fileeg -reference File -istruct reference.maecan be changed on the LiveDesign admin page or from the Parametrize model panel.Input(s): LiveReport Compound structure columnOutput column(s) in the LiveReport: The lowest energy conformations are reported back in the LiveReport as poses as well as a column with the corresponding relative energies. These are also includedin the pose name. Compound structure input protocol conformationsLiveDesignCompound structures from the LiveReport New LiveReport column(s):- Ligand conformations- Relative energyConfGen(otherwise MacroModel)%input%Alignment reference%input%Number of conformers%input%DisabledCommandOutput 32162 LigPrep options%input%and pose renaming-istruct reference.maeCheck the alignment reference structureVisual inspectionof the alignment Upload asLiveDesign Model MacroModelConformational Search Lowest energy CredentialsConfiguration SDF Reader 3D coordinates Column Filter Boolean Input StringConfiguration IntegerConfiguration ConfGen Config Table Viewer Table Viewer Test locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) StringConfiguration Alignment Alignment Table Viewer Run Maestro LiveDesign Input This workflow is uploaded as Computational model when executing the Upload model to LiveDesign node. The KNIME workflow can then be run in LiveDesign on the LiveReport structures. The output column(s) will be added to the LiveReport. Changelog:22.2.4 - Automatic protocol selection and installation21.2.1 - MacroModel structures are aligned as well21.2.0 - Control to generate several LigPrep forms Uses Primary_host and 1 CPU21.1.2 - Better pose naming21.1.1 - Alignment on a core section Energy difference in kcal/mol Lowest conformations from MacroModel20.4.1 - ConfGen branch Alignment on a reference specified in the admin page (file or corporate ID) Adapted to the energy column name change in 21-1 Parameter(s) which can be changed from the Admin page or the Parametrized model panel:- The LigPrep optionsIn quotes: eg -ligprepOptions "-s 4 -epik -pht 2". See $SCHRODINGER/ligprep -h message- The conformational search method (ConfGen of MacroModel)eg -ConfGen true- The number of conformers eg -max_num_conformers 10- The aligment reference or core fileeg -reference File -istruct reference.maecan be changed on the LiveDesign admin page or from the Parametrize model panel.Input(s): LiveReport Compound structure columnOutput column(s) in the LiveReport: The lowest energy conformations are reported back in the LiveReport as poses as well as a column with the corresponding relative energies. These are also includedin the pose name. Compound structure input protocol conformationsLiveDesignCompound structures from the LiveReport New LiveReport column(s):- Ligand conformations- Relative energyConfGen(otherwise MacroModel)%input%Alignment reference%input%Number of conformers%input%DisabledCommandOutput 32162 LigPrep options%input%and pose renaming-istruct reference.maeCheck the alignment reference structureVisual inspectionof the alignment Upload asLiveDesign Model MacroModelConformational Search Lowest energy CredentialsConfiguration SDF Reader 3D coordinates Column Filter Boolean Input StringConfiguration IntegerConfiguration ConfGen Config Table Viewer Table Viewer Test locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) StringConfiguration Alignment Alignment Table Viewer Run Maestro LiveDesign Input

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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: 2020-01-31
On NodePit since: 2021-08-05
Last update: 2024-04-24
Created with KNIME version: v4.6.1
Tags: LiveDesignLigPrepMacroModelConfGenSchrodinger

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