Icon

Docking and rendering

Docks the compounds with Glide and changes the rendering of the binding site (atoms displayed, residues labelled and the atom representation) to highlight important residues.

[32291] 22.2.4
See details in https://kni.me/w/hgBob9Gyg256DKes

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 LigPrep options Uses Primary_host and 1 CPU20.4.1 - The number of poses per ligand can be controlled fromLiveDesign admin panel. Input(s): LiveReport Compound structure columnConfiguration(s) controlled from the Admin panel or the Parametrize model panel:- The LigPrep optionsIn quotes: eg -ligprepOptions "-s 4 -epik -pht 2". See $SCHRODINGER/ligprep -h message- Glide grideg -igrd Protein_Glide_grid.zip- Number of docking poses in the outputeg -POSES_PER_LIG 2Output column(s) in the LiveReport:- Docked poses- Docking scores Binding siteonly %input% Compound structure input protocol.Docked pose outputImportant onesNo proteinRendering checkingImportant onesin ball and stick LiveDesignCompound structures from the LiveReportCompound structure input protocolCompound structuresfrom LiveDesignNumber of poses%input%LigPrep options%input%PreparationDisplay atoms Glide LigandDocking Glide Grid Reader Upload asLiveDesign Model Apply labels -Residue information Row Splitter Run Maestro Atom representation 3D coordinates CredentialsConfiguration SDF Reader Upload asLiveDesign Protocol LiveDesign Input String Manipulation(Variable) IntegerConfiguration StringConfiguration Output columns 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 LigPrep options Uses Primary_host and 1 CPU20.4.1 - The number of poses per ligand can be controlled fromLiveDesign admin panel. Input(s): LiveReport Compound structure columnConfiguration(s) controlled from the Admin panel or the Parametrize model panel:- The LigPrep optionsIn quotes: eg -ligprepOptions "-s 4 -epik -pht 2". See $SCHRODINGER/ligprep -h message- Glide grideg -igrd Protein_Glide_grid.zip- Number of docking poses in the outputeg -POSES_PER_LIG 2Output column(s) in the LiveReport:- Docked poses- Docking scores Binding siteonly %input% Compound structure input protocol.Docked pose outputImportant onesNo proteinRendering checkingImportant onesin ball and stick LiveDesignCompound structures from the LiveReportCompound structure input protocolCompound structuresfrom LiveDesignNumber of poses%input%LigPrep options%input%PreparationDisplay atoms Glide LigandDocking Glide Grid Reader Upload asLiveDesign Model Apply labels -Residue information Row Splitter Run Maestro Atom representation 3D coordinates CredentialsConfiguration SDF Reader Upload asLiveDesign Protocol LiveDesign Input String Manipulation(Variable) IntegerConfiguration StringConfiguration Output columns

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: jcmozzic
Created at: 2020-01-31
On NodePit since: 2020-08-12
Last update: 2024-04-26
Created with KNIME version: v4.6.1
Tags: LiveDesignGlideLigPrepSchrodinger

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!