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View PDB Structures

This workflow allows to interactively explore in 3D the PDB structure with the small molecule ligand.

The RCSB PDB is accessed via the PDB Connector Query Builder node. It allows to build an advanced query webservice and closely follows the web UI at https://www.rcsb.org/search/advanced
See the documentation of the node and the web UI for the example queries.

The information about the ligand is extracted using several webserivices via the GET Request nodes.

The 3D view of the protein structure and the ligand structure is generated using the 3Dmol.js librarydeveloped by N.Rego and D.Koes. Note that only selected formates are supported for the visualization: PDB, SDF, MOL2, XYZ, and CUBE formats.


Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829


Required extenstions: KNIME Chemistry Base Types and Nodes, RDKit Nodes feature, Vernalis KNIME Nodes

Get most recently published PDB entries Get info about proteins and ligands from PDB Fetch PDB files Fetch ligand structural data Display structures View PDB StructuresThis workflow allows to interactively explore in 3D the PDB structure with the small molecule ligand. For more information see workflow Description. View >> DescriptionRequired extenstions: KNIME Chemistry Base Types and Nodes, RDKit Nodes feature, Vernalis KNIME Nodes create URLextract info on the ligandchem cpd name and weightLatestget smilesfirst 200pick largest ligandfrom each structureremove no ligand structuresextract SMILESof the ligandcreate URLAccepted formats:PDB, SDF, MOL2 PDB ConnectorQuery Executor Column Expressions GET Request JSON to Table JSON Path Ungroup PDB ConnectorQuery Builder JSON Path Row Filter DuplicateRow Filter Row Filter GET Request PDB Downloader String Manipulation Molecule Type Cast PDB + Ligand viewer Get most recently published PDB entries Get info about proteins and ligands from PDB Fetch PDB files Fetch ligand structural data Display structures View PDB StructuresThis workflow allows to interactively explore in 3D the PDB structure with the small molecule ligand. For more information see workflow Description. View >> DescriptionRequired extenstions: KNIME Chemistry Base Types and Nodes, RDKit Nodes feature, Vernalis KNIME Nodes create URLextract info on the ligandchem cpd name and weightLatestget smilesfirst 200pick largest ligandfrom each structureremove no ligand structuresextract SMILESof the ligandcreate URLAccepted formats:PDB, SDF, MOL2PDB ConnectorQuery Executor Column Expressions GET Request JSON to Table JSON Path Ungroup PDB ConnectorQuery Builder JSON Path Row Filter DuplicateRow Filter Row Filter GET Request PDB Downloader String Manipulation Molecule Type Cast PDB + Ligand 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: glandrum
Created at: 2020-11-11
On NodePit since: 2020-12-17
Last update: 2025-05-22
Created with KNIME version: v4.5.0
Tags: Life SciencesRDKitcheminformaticsPDBSDFGET RequestJSON3D view

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