Scheduled Seminars on 3/3/2011

SUNGHWAN KIM at 11:00  Edit  Reschedule  Delete

PubChem, a free and open archive for the biological activities of small molecules, contains 70 million substance descriptions, 28 million unique small molecules, 480,000 biological assays, and 110 million biological assay outcomes. When possible, PubChem generates a theoretical 3-D conformer model description for each and every record in the PubChem Compound database contains. This 3-D layer is the basis of the PubChem3D project. PubChem3D also pre-computes 3-D “Similar Conformers” neighboring relationships to identify compounds with similar 3-D shape and pharmacophore features, helping the users to locate similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods. Currently, the first two diverse 3-D conformers of 26.1 million PubChem Compound records has been compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion 3-D conformer neighbor pairs and 6.62 billion 3-D compound neighbor pairs, with an average of 253 “Similar Conformers” compound neighbors per compound. In this presentation, I will describe various aspects of the PubChem3D project, including strategies used for conformer generation and 3-D neighboring.

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