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Public Cheminformatics Database (PubChem)

PubChem is a public database with annotated information about the biological activities of compounds in the Molecular Libraries Small Molecule Repository (MLSMR) as well as chemical structures and compound probe information.

PubChem was created on behalf of the Molecular Libraries Roadmap Initiative by the National Center for Biotechnology Information (NCBI). Various data, including records on substances and compounds and assay screening, are organized in three linked databases within the NCBI’s Entrez information retrieval system: PCSubstance, PCCompound, and PCBioAssay.

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 depositor web sites provide further information on PubChem depositors. The databse also provides a fast chemical structure similarity search tool.

A PubChem FTP site and Deposition Gateway are also available.

PubChem in the Pilot Phase of ML

For the pilot phase, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points – and over 250 bioassays, a good percentage of which were contributed by the Molecular Libraries Screening Centers.

A related cheminformatics initiative, during the pilot phase, is developing novel cheminformatics tools, improved methods of investigation and approaches to cheminformatics research, and creative ways of translating learned experience to the larger biomedical research community.

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