Saturday, October 20, 2007

PubChem: A Public Chemical Portal

PubChem provides information on the biological activities of small molecules. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively.

PubChem Substance: Search deposited chemical substance records using names, synonyms or keywords. Links to biological property information and depositor web sites are provided. The PubChem substance database contains chemical structures, synonyms, registration IDs, description, related ... [Web sites], database cross-reference links to PubMed, protein 3D structures, and biological screening results. If the contents of a chemical sample are known, the description includes links to PubChem Compound.

PubChem Compound: Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound. The PubChem Compound Database contains validated chemical depiction information that is provided to describe substances in PubChem Substance. Structures stored within PubChem Compound are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.Users can perform a term/keyword search in a same manner as for substance database. In addition, the PubChem compound database also provides a chemical property search.

PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example "cancer cell line". Links to active compounds and bioassay results are provided. The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to a screening protocol.

Structure Search: Search PubChem's Compound database using a chemical structure as the query. PubChem Structure Search allows PubChem Compound Database to be queried using a chemical structure. Chemical structure queries may be sketched using the PubChem Sketcher. You may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.

The Substance/Compound database, where possible, provides links to bioassay description, literature, references, and assay data points. The BioAssay database also includes links back to the Substance/Compound database.

PubChem Help
This document provides tips and examples for searches of the three PubChem databases by text term/keyword, as well as tips for searching PubChem Compound by chemical properties.


PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features.

PubChem is a component of NIH's Molecular Libraries Roadmap Initiative.

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