Scheduled Seminars on 12/14/2010

JIE CHEN at 11:00  Edit  Reschedule  Delete

Exploring chemical molecules with PubChem 3D resourcesTBD
3-dimensional structures of chemical molecules are important to their functions. Structural similar molecules are likely to have similar biological and physicochemical characteristics. This basic belief is the key concept in ligand-based drug design to find potential drug leads at the very beginning of the drug discovery and development. In addition to employing 2D similarity relationships to determine chemical analogs, PubChem provides various powerful tools , algorithms and 3D neighboring data to assist the discovery of chemicals with similar 3D shape and feature orientations, and enhance the understanding of results from different research activities. The PubChem 3D viewing makes the integrated information on chemical structures easily accessible and understandable to various users with diverse background. It involves the display of the 3D structure of a compound conformer and of superposition of similar conformers (known as the fit conformers) for each compound (known as the reference conformer). The 3D information on chemical molecules and neighboring can be downloaded from PubChem 3D services. Such information consists of new 3D properties, including MMFF partial charges, volume, steric quadrupoles moments, steric octopole moments and MMFF94 energy. The PubChem 3D viewing is also being widely applied into different projects in PubChem to improve the performance of this giant as a whole . This presentation will detail the development of the PubChem 3D resources.


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