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3D View of PDB structures

This workflow snippet demonstrates how to query PDB using the PDB nodes from the Vernalis extension and to visualized the results in 3D using the 3D Molecule Viewer component. If you combine the 3D Molecule Viewer component with a Table View node in a component, the two views interact and the selection from the Table view is displayed in the 3D Molecule Viewer.

Required Extensions:
- Vernalis KNIME Nodes



3D View of PDB structuresThe wiorkflow demonstrates how to query PDB using the PDB nodes from the Vernalis extension and visualising the structures in 3D using the 3DMolecule Viewer component combined with a Table view node. PDB ConnectorQuery Builder PDB ConnectorQuery Executor PDB Downloader PDB PropertyExtractor Data Table with 3DMolecule Viewer 3D View of PDB structuresThe wiorkflow demonstrates how to query PDB using the PDB nodes from the Vernalis extension and visualising the structures in 3D using the 3DMolecule Viewer component combined with a Table view node. PDB ConnectorQuery Builder PDB ConnectorQuery Executor PDB Downloader PDB PropertyExtractor Data Table with 3DMolecule Viewer

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: janinamothes
Created at: 2021-01-07
On NodePit since: 2021-12-18
Last update: 2026-01-23
Created with KNIME version: v4.3.0
Tags: PDBCheminformatics3DLife Sciences

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