PubChem is an open repository for small molecules and their experimental biological activities, which was launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the U.S. National Institutes of Health.  PubChem integrates chemical information from various depositors and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of the contributed information.  PubChem is a sizeable system with more than 117 million substance descriptions, 46 million unique small molecules, 647 thousand biological assays, covering thousands of protein targets.  Currently it has more than 110,000 users everyday on average.        The PubChem3D project aims to assist in the analysis of biologically similar molecules that are difficult to interrelate using traditional 2-D similarity methods.  It generates a 3-D conformer model for ~92% of chemical records in PubChem.  A pre-computed multi-conformer 3-D similarity search for each chemical gives immediate access to a set of structurally similar compounds in PubChem as well as their respective superpositions.  The PubChem3D Structure-Activity Relationship (SAR) Cluster database helps one to discover useful bioactivity data patterns.  In conjunction with the rich annotation available in PubChem, such as experimental 3-D structure, relevant patent documents, cited scientific literature, and medication information, one can quickly navigate the structurally similar compounds that share common annotations.  In addition, PubChem's location at the National Center for Biotechnology Information (NCBI) allows the user to readily access integrated pertinent information beyond that found in PubMed, such as protein target, gene, disease, and pathway.        The coupling of PubChem's massive collection of chemical and bioactivity information with SAR analysis capabilities helps present new opportunities for the biomedical research community to facilitate chemical probe development and drug discovery.  This presentation will provide an overview of the PubChem3D resources and demonstrate their utility for finding useful bioactivity data patterns.

PubChem and PubChem3D: Public chemical information resources for biological assay data analysis and drug discovery

246th National Meeting (2013)

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