Analyze small molecule interactions in the PDB with Ligand Explorer
Ligand Explorer can display hydrogen bonds, hydrophobic interactions, bridged H-bonds, metal interactions, and neighbor residue interactions and thresholds in a dynamic viewer.
Users can 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 an image file, or as a text file listing interactions.
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.