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

Bioinformatics. 2005 Nov 15;21(22):4133-9. doi: 10.1093/bioinformatics/bti683. Epub 2005 Sep 20.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Access to Information*
  • Chemistry / methods*
  • Chemistry, Organic / methods
  • Computational Biology
  • Databases, Factual*
  • Databases, Genetic
  • Genomics
  • Health Resources
  • Information Storage and Retrieval*
  • Internet
  • Models, Chemical
  • Models, Statistical
  • Natural Language Processing
  • Sequence Alignment
  • User-Computer Interface