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

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 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 contains substance and bioassay information from a multitude of depositors.

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