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Bioinformatics Advance Access published online on April 1, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth214
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received December 12, 2003
Revised March 3, 2004
Accepted March 3, 2004

Applications note

Ligand Depot: a data warehouse for ligands bound to macromolecules

Zukang Feng 1, Li Chen 1, Himabindu Maddula 1, Ozgur Akcan 1, Rose Oughtred 1, Helen M. Berman 1, John Westbrook 1*

1 Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854

* To whom correspondence should be addressed. E-mail: jwest{at}rcsb.rutgers.edu.


  Abstract

Summary: 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 http://ligand-depot.rutgers.edu/. 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.


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