ChemDB


17599932	ChemDB update--full-text search and virtual chemical space. [PMID: 17599932] Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P. 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Bioinformatics. 2007:23(17) \| 55 Citations (from Europe PMC, 2025-03-22)
16174682	ChemDB: a public database of small molecules and related chemoinformatics resources. [PMID: 16174682] Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P. Abstract 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 http://cdb.ics.uci.edu. Bioinformatics. 2005:21(22) \| 56 Citations (from Europe PMC, 2025-03-22)

ChemDB update--full-text search and virtual chemical space. [PMID: 17599932]

Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P.

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.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bioinformatics. 2007:23(17) | 55 Citations (from Europe PMC, 2025-03-22)

ChemDB: a public database of small molecules and related chemoinformatics resources. [PMID: 16174682]

Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P.

Abstract

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 http://cdb.ics.uci.edu.

Bioinformatics. 2005:21(22) | 56 Citations (from Europe PMC, 2025-03-22)

URL:	http://cdb.ics.uci.edu
Full name:	chemical database
Description:	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 chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility.
Year founded:	2005
Last update:	2012
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	Other
Data object:	Animal
Database category:	Health and medicine
Major species:	NA
Keywords:	small molecule drug discovery

University/Institution:	University of California Irvine
Address:	Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, USA
City:	Irvine
Province/State:	California
Country/Region:	United States
Contact name (PI/Team):	Pierre Baldi
Contact email (PI/Helpdesk):	pfbaldi@ics.uci.edu

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases