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Bioinformatics Advance Access originally published online on June 28, 2007
Bioinformatics 2007 23(17):2348-2351; doi:10.1093/bioinformatics/btm341
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ChemDB update—full-text search and virtual chemical space

Jonathan H. Chen , Erik Linstead , S. Joshua Swamidass , Dennis Wang and Pierre Baldi *

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

*To whom correspondence should be addressed.


  Abstract

ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB.

Availability: ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu.

Contact: pfbaldi{at}ics.uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Chris Stoeckert

Received on April 4, 2007; revised on June 4, 2007; accepted on June 21, 2007

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