ChemDB update - Full-text search and virtual chemical space

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

Research output: Contribution to journalArticlepeer-review

93 Scopus citations


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.

Original languageEnglish
Pages (from-to)2348-2351
Number of pages4
Issue number17
StatePublished - Sep 1 2007


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