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Ligand alignment by shape with a flexible reference

Aligns ligands on a reference structure treated flexibly as well, using Shape screening.

[32102] 22.2.4
See more details on https://kni.me/w/aVt4hyxyM8IAAKak

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 computationallyexpensive calculations Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or theParametrized model panel:- The ligand reference file-istruct Template.sdfOutput column(s) in the LiveReport: - 3D structures aligned, with the template structure as second pose %input%Ligand template file-istruct Template.sdf Compound structure input protocolPharmacophorevolume scoring,Best alignment onlyLiveDesignCompound structures from the LiveReport Visual checking Corporate ID and new LiveReport column(s):- 3D structure alignmentwith the reference structureas second poseDisabledCommandOutput 32102Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model Shape Screening CredentialsConfiguration SDF Reader Run Maestro Conformation search Best alignment Testing Table Viewer Table Viewer Test locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) 3D coordinates 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 installation21.2.0 - Control the distribution of the computationallyexpensive calculations Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or theParametrized model panel:- The ligand reference file-istruct Template.sdfOutput column(s) in the LiveReport: - 3D structures aligned, with the template structure as second pose %input%Ligand template file-istruct Template.sdf Compound structure input protocolPharmacophorevolume scoring,Best alignment onlyLiveDesignCompound structures from the LiveReport Visual checking Corporate ID and new LiveReport column(s):- 3D structure alignmentwith the reference structureas second poseDisabledCommandOutput 32102Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model Shape Screening CredentialsConfiguration SDF Reader Run Maestro Conformation search Best alignment Testing Table Viewer Table Viewer Test locally theLiveDesign KNIME model Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) 3D coordinates 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: 2021-02-16
Last update: 2024-12-17
Created with KNIME version: v4.6.1
Tags: LiveDesignShape screeningLigPrepSchrodinger

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