W0084

LigandDepot: An Information Resource for Small Molecules. Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Helen M. Berman and John Westbrook, PDB, Dept. of Chemistry and Chemical Biology, Rutgers, The State Univ. of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087 USA.

The LigandDepot is an integrated data resource for finding information about small molecules that bind to proteins and nucleic acids.

Information about these small molecules is available from a wide variety of Web resources. LigandDepot provides a single, intelligent user interface across this diverse collection. LigandDepot stores information about these resources in a local database. It accepts queries on molecular name, chemical formula, SMILES string, and CAS registry number, and presents the results extracted from the different sites. LigandDepot also provides a graphical interface that searches for structures or substructures using molecular diagrams. Structures encoded in common small data formats, like MOL2, and the mmCIF format used by the Protein Data Bank can be imported and exported by the drawing interface. The graphical user interface provides an efficient means for creating and editing complex queries of molecular structure.

The LigandDepot currently stores information from 70 small molecule sites. The supporting local database contains detailed chemical descriptions for the 4000 small molecules in the PDB and the 250,000 molecules identified as potential drug targets by National Cancer Institute.

This work was supported by the State of NJ Commission on Higher Education, Rutgers' Strategic Resources and Opportunity Analysis project and by funds that support the PDB from the NSF, the DOE, and two units of the NIH: the NIGMS and the NLM.