NAR Molecular Biology Database Collection entry number 1023
Chen J.H., Swamidass S.J., Dou Y., Linstead E. and Baldi P.
Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine

Database Description

ChemDB ( is a public database of small molecules available over the Web. These 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. 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 over 4M commercially available compounds. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities

Recent Developments

Chemical structural (and substructure) similarity search algorithms have been optimized to allow for searching through over 4M records within seconds. Full-text indexing of vendor annotations has been added allowing for powerful text-based searches, such as finding chemicals by their systematic and common names. Searching through "virtual chemical space" is enabled by applying retrosynthetic reaction models to target molecules and then reconstructing hypothetical products from the proposed precursors.


Work supported by an NIH Biomedical Informatics Training grant (LM-07443-01) and an NSF MRI grant (EIA-0321390) to PB, by the UCI Medical Scientist Training Program, and by a Harvey Fellowship to S.J.S. Academic software license provided by OpenEye Scientific Software for their Python OEWrappers module. The JME editor is provided courtesy of Peter Ertl, Novartis. Additional software provided by the OpenBabel and JMol projects. We would also like to thank Drs. Chamberlin, Nowick, Piomelli, and Weiss for their useful feedback.


1. Jonathan Chen, S Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi (2005). ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources, Bioinformatics 21: 4133-4139.

Subcategory: Small molecules

Go to the abstract in Bioinformatics, 2005, 22, 4133-4139
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