When: Friday, April 29, 2005, 12:00 noon

Where: Room 501,  IS Building

Who: Xiong Liu, DIST, University of Pittsburgh

Title: A High Throughput Web Database for Protein Functional Motion Analysis

Abstract: Detailed understanding of protein function and its interactions with other molecules is one of the major objectives of bioinformatics in the post-genomic era. Function is a dynamic property closely related to the conformational mechanisms of the protein structure in its physiological environment. Time performance of molecular simulations has been a major hurdle for a systematic computational characterization of protein dynamics. Efficient methods and tools for predicting collective motions at the molecular level are becoming increasingly important for understanding and controlling the function of target proteins.

I introduce an efficient approach to predict conformational dynamics, and therefore a high throughput Web database system called iGNM for dynamic and functional analysis of all known protein structures ranging from enzymes to large complexes and assemblies in a unified framework. iGNM is expected to benefit bioinformatics researchers, healthcare personnel and pharmaceutical companies in general. System architecture and components are discussed. Also, illustrative examples and an application to enzymes are presented to demonstrate the utility of the system.

Short bio: Xiong Liu is a Phd candidate in the Department of Information Science and Telecommunications at University of Pittsburgh. His research interests include bioinformatics, biomedical databases, spatial databases, data mining, web services and grid computing.