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Bioinformatics Advance Access originally published online on September 20, 2005
Bioinformatics 2005 21(22):4133-4139; doi:10.1093/bioinformatics/bti683
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ChemDB: a public database of small molecules and related chemoinformatics resources

Jonathan Chen 1,2,{dagger}, S. Joshua Swamidass 1,2,{dagger}, Yimeng Dou 1,2, Jocelyne Bruand 1,2 and Pierre Baldi 1,2,*

1Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California Irvine, CA, USA
2Department of Computer Science, School of Information and Computer Sciences, University of California Irvine, CA, USA

*To whom correspondence should be addressed.

Motivation: The development of chemoinformatics has been hampered by the lack of large, publicly available, comprehensive repositories of molecules, in particular of small molecules. Small molecules play a fundamental role in organic chemistry and biology. They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds.

Results: We describe ChemDB, a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities.

Availability: Database and datasets are available on http://cdb.ics.uci.edu

Contact: pfbaldi{at}ics.uci.edu

Supplementary information: Supplementary materials are available on http://cdb.ics.uci.edu

Received on July 10, 2005; revised on September 11, 2005; accepted on September 18, 2005

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