PubChem, released in 2004, provides information on the biological activities of small molecules.

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.

Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties. These include links to PubMed scientific literature and NCBI's protein 3D structure resource. Links to PubChem's bioassay database present the results of biological screening. Links to depositor web sites provide further information. A PubChem FTP site, Download Facility, Power User Gateway(PUG), Standardization Service, Score Matrix Service, Structure Clustering, and Deposition Gateway are also available.

PubChem provides tips and example code to allow users to add PubChem search tool (free) in their sites. A PubChem publication site provides links to published articles.