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Ligand alignment by shape with a cocrystallized reference

Aligns ligands on a rigid template structure using Shape screening.

[32301] 22.2.4
See more details on https://kni.me/w/vh64HxBIkrZ2VGZo


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 calculations21.1.0 - Added the Shape similarity column Input(s): LiveReport Compound structure columnParameter(s) which can be changed from the Admin page or theParametrized model panel: - The ligand reference fileOutput column(s) in the LiveReport: - 3D structures aligned, with the template structure as second pose- Shape similarity score %input%Ligand template file-istruct Template.maegz Compound structure input protocolLiveDesignCompound structures from the LiveReport Visual checking Corporate ID and new LiveReport column(s):- 3D structures alignedwith the querystructureas second pose- Shape similarity score 100 conformers,no minimization Volume scoring: PharmacophoreBest alignment onlyDisabledCommandOutput 32301Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model CredentialsConfiguration SDF Reader Run Maestro Include thereference Column Filter ConfGen Ungroup MAE Shape Screening 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 computationally expensive calculations21.1.0 - Added the Shape similarity column Input(s): LiveReport Compound structure columnParameter(s) which can be changed from the Admin page or theParametrized model panel: - The ligand reference fileOutput column(s) in the LiveReport: - 3D structures aligned, with the template structure as second pose- Shape similarity score %input%Ligand template file-istruct Template.maegz Compound structure input protocolLiveDesignCompound structures from the LiveReport Visual checking Corporate ID and new LiveReport column(s):- 3D structures alignedwith the querystructureas second pose- Shape similarity score 100 conformers,no minimization Volume scoring: PharmacophoreBest alignment onlyDisabledCommandOutput 32301Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model CredentialsConfiguration SDF Reader Run Maestro Include thereference Column Filter ConfGen Ungroup MAE Shape Screening 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: 2024-04-25
Created with KNIME version: v4.6.1
Tags: LiveDesignShape screeningLigPrepSchrodinger

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