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The Molecular Libraries Program is an NIH initiative designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers.  Use of the data is defined by the Molecular Libraries IP & Data Sharing Policy.

There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem’s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, 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 pilot phase of the MLP. The deposition will continue during the current MLPCN phase.

PubChem is organized as three linked databases within the NCBI’s Entrez information retrieval system and as such chemical structure records are linked to other resources available within Entrez e.g., PubMed, MMDB (protein 3D structure), etc. PubChem also provides a fast chemical structure similarity search tool.

A PubChem FTP site and Deposition Gateway are also available.

To find Substance or BioAssay submissions from MLPCN (Molecular Libraries Probe Production Center Network) or the pilot phase MLSCN (Molecular Libraries Screening Center Network), or the MLSMR (Small Molecule Repository), click here.

PubChem Power User Gateway (PUG) is released. PUG is an XML-based programmatic interface to PubChem that can perform structure searching and structure download. A SOAP-compliant wrapper is available.

For additional inquiries about PubChem, write to the PubChem helpdesk ( or see the Frequently Asked Questions page.