Icon

Ligand alignment with a cocrystallized reference

It aligns the structures on a reference ligand kept rigid using align_ligands utility.

[32358] 22.2.4
See more details on https://kni.me/w/W2M5bmcVq2AzDVOW

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 Uses the Ligand alignment node Reports the similarity to the template structure Uses 1 CPU and Primary host Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or theParametrized model panel:- The ligand reference file can be changed on the LiveDesign adminpage or from the Parametrize model panel.Output column(s) in the LiveReport: - 3D structures aligned, with the reference structure as second pose %input%Ligand template file-istruct Template.maegzCompound structure input protocolLiveDesignCompound structures from the LiveReport Visual checkingutilities/align_ligandsOptionsAlignment on the largest Bernis-Murcko scaffoldof a rigid reference ligandRuns align_ligand -refDisabledCommandOutput 32358 Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model CredentialsConfiguration SDF Reader Run Maestro Get Help Table Viewer Ligand Alignment Config Table Viewer Table Viewer Testing Include thereference 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 Uses the Ligand alignment node Reports the similarity to the template structure Uses 1 CPU and Primary host Input(s): LiveReport Compound structure columnParameter(s) that can be changed from the Admin page or theParametrized model panel:- The ligand reference file can be changed on the LiveDesign adminpage or from the Parametrize model panel.Output column(s) in the LiveReport: - 3D structures aligned, with the reference structure as second pose %input%Ligand template file-istruct Template.maegzCompound structure input protocolLiveDesignCompound structures from the LiveReport Visual checkingutilities/align_ligandsOptionsAlignment on the largest Bernis-Murcko scaffoldof a rigid reference ligandRuns align_ligand -refDisabledCommandOutput 32358 Compound structure input protocol Compound structuresfrom LiveDesignMolecule Reader(to MAE) Upload asLiveDesign Model CredentialsConfiguration SDF Reader Run Maestro Get Help Table Viewer Ligand Alignment Config Table Viewer Table Viewer Testing Include thereference Upload asLiveDesign Protocol CASE Switch Data(Start) (deprecated) 3D coordinates LiveDesign Input

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: 2021-02-16
Last update: 2024-11-18
Created with KNIME version: v4.6.1
Tags: LiveDesignLigPrepSchrodinger

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

Try NodePit Runner!