Icon

Get PDB and preparation

Get PDB and Protein preparation

Downloads the structure for the PDB IDs listed in the selected Free Form Column from the LiveReport, optinoally prepare the structures, extracts and creates new columns with the structures and corresponding structural information.

[32198] version 22.2.0
Find more information from https://kni.me/w/noNj5ZU3Mw2XYOf4

Input: PDB IDs in a string or a Free Form ColumnConfiguration from LiveDesign admin page or from the Parametrize model panel:- the structure source: PDB or other source link- Protein preparation or not- Aligment on a reference structureOutput column(s):- Protein-ligand complex - PDB resolution, deposition date- PDB title, chains, classification Changelog:22.2.0 - LiveDesign input node and testing section22.1.1 - Robustness improvements21.3.0 - Operates on a FFC and string column21.2.0 - Robustness improvements 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 data. The output column(s) will be added to theLiveReport.Clean upLiveDesignPreparation and minimizationProtein preparation%input%Minimization%input% and pose nameStructure source%input%Reference structure%input% Column inputprotocol.Receptor-ligand complexes as output Testing scenariosColumns from the LiveReportwhen run in LiveDesignPrototyping: Corporate IDand PDB ID And input protection or testing Protein PreparationWizard CredentialsConfiguration Protein PreparationWizard StringConfiguration StringConfiguration Switch PDB information StringConfiguration StringConfiguration Alignment Upload asLiveDesign Model Upload asLiveDesign Protocol Table Creator LiveDesign Input Table Creator Get PDB structures CASE Switch End In LiveDesignand prototyping Output columns Input: PDB IDs in a string or a Free Form ColumnConfiguration from LiveDesign admin page or from the Parametrize model panel:- the structure source: PDB or other source link- Protein preparation or not- Aligment on a reference structureOutput column(s):- Protein-ligand complex - PDB resolution, deposition date- PDB title, chains, classification Changelog:22.2.0 - LiveDesign input node and testing section22.1.1 - Robustness improvements21.3.0 - Operates on a FFC and string column21.2.0 - Robustness improvements 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 data. The output column(s) will be added to theLiveReport.Clean upLiveDesignPreparation and minimizationProtein preparation%input%Minimization%input% and pose nameStructure source%input%Reference structure%input% Column inputprotocol.Receptor-ligand complexes as output Testing scenariosColumns from the LiveReportwhen run in LiveDesignPrototyping: Corporate IDand PDB ID And input protection or testing Protein PreparationWizard CredentialsConfiguration Protein PreparationWizard StringConfiguration StringConfiguration Switch PDB information StringConfiguration StringConfiguration Alignment Upload asLiveDesign Model Upload asLiveDesign Protocol Table Creator LiveDesign Input Table Creator Get PDB structures CASE Switch End In LiveDesignand prototyping 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: 2021-11-16
Last update: 2024-12-17
Created with KNIME version: v4.5.1
Tags: LiveDesignPPrepSchrodinger

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

Try NodePit Runner!