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Article

The PubChem Project

Jerome Pansanel  (16 February 2006)

The PubChem Project provides information on the biological activities of small molecules. It is a component of NIH’s Molecular Libraries Roadmap Initiative. Government information available from this site is within the public domain.

PubChem is organized in three primary databases that can be retrieved on the FTP depository:
- PubChem Compound
- PubChem Substance
- PubChem BioAssay

PubChem also provides a fast chemical structure similarity search tool.

PubChem Compound. The PubChem Compound database contains more than 5 million unique structures. Chemical structure can be searched by using names, synonyms or keywords. Links to available biological property information are provided for each compound. In addition, where possible, links to bioassay description, literature, references, and assay data points are also provided.

PubChem Substance. The PubChem Substance database contains more than 8 million records. Chemical substance record can be searched by using names, synonyms or keywords. Links to biological property information and depositor web sites are provided. In addition, where possible, links to bioassay description, literature, references, and assay data points are also provided.

PubChem BioAssay. The PubChem BioAssay database contains more than 190 bioassays. Each bioassay contains a various number of data points. Bioassay record can be explored by using terms from the bioassay description ("cancer cell line", i.e.). Links to active compounds and bioassay results are provided.

Structure Search. This tool enables searching for structure in the PubChem’s Compound database by using a chemical structure as the query. Structures may be sketched or specified by SMILES, MOL files, or other formats (most standard and common chemical file formats may be used, including "SDF", "CDX", "SKC", "MOL2", "JME", and "SK2"). An advance search formular is also available.

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