RCSB PDB Newsletter #20: Ligand Depot--a Small Molecule Information Resource

No. 20
Winter 2004


Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank

Downloadable PDB_EXTRACT Makes Deposition Easier

Biological Unit Tutorial Now Available from the RCSB PDB

Ligand Depot--a Small Molecule Information Resource

PDB Focus: Deposition and Release Policies

PDB Deposition Statistics

Lucene Keyword Search Released on the RCSB PDB Web Site

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

PDB Focus: Searching for Experimental Data Files

Updates of mmCIF Files on the RCSB PDB FTP Site

RCSB PDB Web Site Statistics

NIGMS News: PSI-2 and Structural Biology Roadmap RFA

RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

Related Links: FTP Resources

RCSB PDB Job Listings

RCSB PDB Members & Statement of Support

Questions? info@rcsb.org

© 2004 RCSB PDB


Ligand Depot--a Small Molecule Information Resource

The Ligand Depot interface

Ligand Depot (ligand-depot.rutgers.edu) is a data warehouse that integrates databases, services, and tools related to small molecules bound to macromolecules. The initial release (v. 1.0, November, 2003) focuses on providing chemical and structural information for ligands that are found as part of the structures deposited with the PDB.

Ligand Depot allows users to extract ligand information from the PDB, to perform chemical substructure searches, and to search other small molecule resources on the Web. One of the distinguishing features of Ligand Depot is that it allows users to retrieve the coordinates of any small molecule found within the structure entries of the PDB. It is also updated daily and therefore provides the most current information on small molecules present in the PDB.

Ligand Depot currently includes chemical descriptions for the ~4,600 ligands that are part of the structures deposited in the PDB, and it offers various search options for obtaining information on these small molecules. It accepts keyword queries based on PDB ligand code, compound name and chemical formula. Using a simple graphical interface, a substructure search may also be performed between a small molecule of interest and all of the ligands present in the PDB.

Ligand Depot can also be used to browse a variety of other small molecule resources on the Web. Information from 70 small molecule sites are stored in Ligand Depot. These resources are organized into four categories, including molecular visualization sites, commercial sites, nomenclature sites, and chemical databases. Keyword searches may be performed on these external Web sites if they are search-enabled. Thus, information on ligands can be extracted from a diverse collection of Web resources using a single query.

A helpful tutorial for using Ligand Depot is accessible at