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

External resources

• PDB advanced search
• 3Dmol.js