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Binding pose strain

It minimizes the binding pose conformation to a local minimum and runs a conformational search to find the global minimum.
The energy difference between the local and the global minima is calculated. The global and local minimum conformations are aligned on the initial binding pose.

[32148] 22.2.0
https://kni.me/w/l1C33ns7BggmDXC5

Input: Select a pose-viewer 3D column from a docking in the LiveReport.Parameter(s) which can be changed from the Admin page or the Parametrized model panel:- Alignment on a specified section of the ligandsStructure to be loaded in Extra file 1 field. By default the alignment is performed on the whole ligandstructure.Output columns in the LiveReport:- Global and local minimum conformations on top of the the initial binding pose.- Local-global minimum conformation energy difference (in kcal/mol) Changelog:22.4.0 - Automatic protocol selection and installation21.4.1 - Conformational search performed for each protonation state21.2.0 - Control the distribution of the computationally expensive calculations21.1.3 - Pose reordering Alignment on each binding pose Optional alignment on a specified section of the ligands21.1.2 - More robust energy difference calculation21.1.1 - Energy difference in kcal/mol20.4.3 - Handles multiple poses in the input Pose name including the energy difference Global and local conformations reported Adapted to the energy column name change in 21-120.4.2 - handles pse input Column inputprotocolLiveDesignAlignmentCheckBy protonationstateCompound structures(exported from the LR) For each ligand Local minimum Global mimimumper pose difference 3D columnPV files(exported independentlyfrom the 3D view) Add the input column(s) to a LiveReport File with the core for the alignment%file%Upload asLiveDesign Model CredentialsConfiguration Run Maestro GroupBy SDF Reader Upload asLiveDesign Protocol Group Loop Start MacroModelMinimization MCS ASL Pose name MacroModelConformational Search Alignment Energy Column Appender LiveDesign Input Ligands only Molecule Reader(to MAE) Output columns For testing Loop End Molecule Reader(to MAE) Input: Select a pose-viewer 3D column from a docking in the LiveReport.Parameter(s) which can be changed from the Admin page or the Parametrized model panel:- Alignment on a specified section of the ligandsStructure to be loaded in Extra file 1 field. By default the alignment is performed on the whole ligandstructure.Output columns in the LiveReport:- Global and local minimum conformations on top of the the initial binding pose.- Local-global minimum conformation energy difference (in kcal/mol) Changelog:22.4.0 - Automatic protocol selection and installation21.4.1 - Conformational search performed for each protonation state21.2.0 - Control the distribution of the computationally expensive calculations21.1.3 - Pose reordering Alignment on each binding pose Optional alignment on a specified section of the ligands21.1.2 - More robust energy difference calculation21.1.1 - Energy difference in kcal/mol20.4.3 - Handles multiple poses in the input Pose name including the energy difference Global and local conformations reported Adapted to the energy column name change in 21-120.4.2 - handles pse input Column inputprotocolLiveDesignAlignmentCheckBy protonationstateCompound structures(exported from the LR) For each ligand Local minimum Global mimimumper pose difference 3D columnPV files(exported independentlyfrom the 3D view) Add the input column(s) to a LiveReport File with the core for the alignment%file% Upload asLiveDesign Model CredentialsConfiguration Run Maestro GroupBy SDF Reader Upload asLiveDesign Protocol Group Loop Start MacroModelMinimization MCS ASL Pose name MacroModelConformational Search Alignment Energy Column Appender LiveDesign Input Ligands only Molecule Reader(to MAE) Output columns For testing Loop End Molecule Reader(to MAE)

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Created by: jcmozzic
Created at: 2020-01-31
On NodePit since: 2021-03-22
Last update: 2024-11-21
Created with KNIME version: v4.6.1
Tags: LiveDesignMacroModelSchrodinger

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