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Docking and protein surface

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

[32680] 22.2.4
See more details on https://kni.me/w/HYX2kc7MxNuEz0EF

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 Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or the Parametrizedmodel panel:- The Grid fileOutput column(s) in the LiveReport:- Docked poses including the surface- Docking scores Binding siteonly Compound structure input protocolPyMOL surface commandsPose viewer outputImportant ones No protein Rendering checkingTitle Important onesin ball and stick-igrd Protein_Glide_grid.zip%input%LiveDesignCompound structures from the LiveReportCorporate ID and new LiveReport column(s):- Docked posesincluding the surface- Docking scoresDisabledCommandOutput 32680Compound structure input protocol Compound structuresfrom LiveDesign Display atoms Glide LigandDocking Upload asLiveDesign Model Apply labels -Residue information Cross Joiner Row Splitter Concatenate Run Maestro Extract Properties Sitemap surface Atom representation Glide Grid Reader CredentialsConfiguration SDF Reader Column Filter Testing Table Viewer Table Viewer Test locally locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) LiveDesign Input 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 Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or the Parametrizedmodel panel:- The Grid fileOutput column(s) in the LiveReport:- Docked poses including the surface- Docking scores Binding siteonly Compound structure input protocolPyMOL surface commandsPose viewer outputImportant ones No protein Rendering checkingTitle Important onesin ball and stick-igrd Protein_Glide_grid.zip%input%LiveDesignCompound structures from the LiveReportCorporate ID and new LiveReport column(s):- Docked posesincluding the surface- Docking scoresDisabledCommandOutput 32680Compound structure input protocol Compound structuresfrom LiveDesign Display atoms Glide LigandDocking Upload asLiveDesign Model Apply labels -Residue information Cross Joiner Row Splitter Concatenate Run Maestro Extract Properties Sitemap surface Atom representation Glide Grid Reader CredentialsConfiguration SDF Reader Column Filter Testing Table Viewer Table Viewer Test locally locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) LiveDesign Input 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: 2020-08-12
Last update: 2024-11-21
Created with KNIME version: v4.6.1
Tags: LiveDesignGlideLigPrepSiteMapSchrodinger

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