Analyze small molecule interactions in the PDB with Ligand Explorer

07/26

(Click image to enlarge)
Ligand Explorer can be used to dynamically display the interactions in PDB entry 2w70.

Ligand Explorer (PDF Flyer) displays hydrogen bonds, hydrophobic interactions, bridged H-bonds, metal interactions, and neighbor residue interactions and thresholds in a dynamic viewer.

Toggle interactions on/off, adjust distance thresholds, label interactions by distance, and display all neighbor residues. Distances, angles, and dihedral angles can be analyzed and measured.  The views created can be saved as a text file listing interactions or as an image file (instructions available for creating high resolution images).

Ligand Explorer can be accessed from the Ligand Chemical Component section of an entry's Structure Summary page. The program uses the same Molecular Biology Toolkit¹ as the RCSB PDB's Protein Workshop and Simple Viewer.

Launching Ligand Explorer can install a local copy of the program on your computer, and can be used to read a local PDB file, or access a PDB file directly using the File menu (when online).

¹The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications
(2005) BMC Bioinformatics, 6: 21.

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