TY - JOUR
T1 - ChemDB
T2 - A public database of small molecules and related chemoinformatics resources
AU - Chen, Jonathan
AU - Swamidass, S. Joshua
AU - Dou, Yimeng
AU - Bruand, Jocelyne
AU - Baldi, Pierre
N1 - Funding Information:
This work was supported by an NIH Biomedical Informatics Training grant (LM-07443-01) and an NSF MRI grant (EIA-0321390) to P.B., and by the UCI Medical Scientist Training Program and a Harvey Fellowship to S.J.S. We would also like to acknowledge the OpenBabel project and OpenEye Scientific Software for their free software academic license, and Drs Chamberlin, Nowick, Piomelli and Weiss for their useful feedback. Funding to pay the Open Access publication charges for this article was provided by the Institute for Genomics and Bioinformatics at UCI.
PY - 2005/11/15
Y1 - 2005/11/15
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=27944507949&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/bti683
DO - 10.1093/bioinformatics/bti683
M3 - Article
C2 - 16174682
AN - SCOPUS:27944507949
SN - 1367-4803
VL - 21
SP - 4133
EP - 4139
JO - Bioinformatics
JF - Bioinformatics
IS - 22
ER -