Ligand Depot: a data warehouse for ligands bound to macromolecules

Bioinformatics. 2004 Sep 1;20(13):2153-5. doi: 10.1093/bioinformatics/bth214. Epub 2004 Apr 1.


Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot.

Availability: Ligand Depot is available at Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Biopolymers / chemistry
  • Biopolymers / classification
  • Database Management Systems
  • Databases, Protein
  • Information Storage and Retrieval / methods
  • Ligands*
  • Macromolecular Substances / chemistry*
  • Macromolecular Substances / classification*
  • Natural Language Processing*
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • User-Computer Interface*


  • Biopolymers
  • Ligands
  • Macromolecular Substances