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Bioinformatics Advance Access published online on September 20, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti683
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 10, 2005
Revised September 11, 2005
Accepted September 18, 2005

Article

ChemDB: a public database of small molecules and related chemoinformatics resources

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

1 Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine

* To whom correspondence should be addressed.
Pierre Baldi, E-mail: pfbaldi{at}ics.uci.edu


  Abstract

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 over 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 3D structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 M commercially available compounds, 8.2 M counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities.

Availability: Database, datasets, and supplementary materials available through: http://cdb.ics.uci.edu.

*These authors contributed equally.
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