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Docking and ligand strain

Docks the compounds with Glide. The docking pose are minimized to a local minimum and a conformational search is run to find the global minimum.
Calculates the conformation energy difference between the local and the global minima.
Aligns the global and local minimum conformations on the initial binding pose.

[32163] 22.2.4
See more details on https://kni.me/w/A9n-cVAz4wGXJQTS

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 installation21.2.0 Control the distribution of the computationally expensive calculations Pose reordering Alignment on each binding pose Optional alignment on a specified section of the ligands More robust energy difference calculation Input(s): LiveReport Compound structure columnOutput column(s) 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) 1 poseper ligand-igrd Protein_Glide_grid.zip%input%EnergydifferenceGlobal mimimumCompound structures from the LiveReportCore for alignment(none by default)-istruct file.mae%input%AlignmentCheck Local minimumCorporate IDFirst pose Compound structureinput procotol.LiveDesign 32163Compound structure input protocol Compound structuresfrom LiveDesignper pose DisabledOutputCommand preparation Glide LigandDocking Glide Grid Reader Math Formula MacroModelConformational Search SDF Reader Molecule Reader(to MAE) Run Maestro Merge MacroModelMinimization Group Loop Start Row Filter Loop End(deprecated) Pose name Upload asLiveDesign Model CredentialsConfiguration Data processing Test locally locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) LiveDesign Input Alignment MCS ASL Testing Table Viewer Table Viewer Result 3D coordinates 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 installation21.2.0 Control the distribution of the computationally expensive calculations Pose reordering Alignment on each binding pose Optional alignment on a specified section of the ligands More robust energy difference calculation Input(s): LiveReport Compound structure columnOutput column(s) 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) 1 poseper ligand-igrd Protein_Glide_grid.zip%input%EnergydifferenceGlobal mimimumCompound structures from the LiveReportCore for alignment(none by default)-istruct file.mae%input%AlignmentCheck Local minimumCorporate IDFirst pose Compound structureinput procotol.LiveDesign 32163Compound structure input protocol Compound structuresfrom LiveDesignper pose DisabledOutputCommand preparation Glide LigandDocking Glide Grid Reader Math Formula MacroModelConformational Search SDF Reader Molecule Reader(to MAE) Run Maestro Merge MacroModelMinimization Group Loop Start Row Filter Loop End(deprecated) Pose name Upload asLiveDesign Model CredentialsConfiguration Data processing Test locally locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) LiveDesign Input Alignment MCS ASL Testing Table Viewer Table Viewer Result 3D coordinates

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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: 2020-12-17
Last update: 2024-11-21
Created with KNIME version: v4.6.1
Tags: LiveDesignGlideLigPrepMacroModelSchrodinger

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