Speaker: Ivet Bahar
Affiliation: Chemical Eng Dept. Polymer Res Center, Bogazici U,
Date: 10/19/99 - Tuesday
Time & Location - 4:15PM, B14 Hollister
Title: Some Computational Tools for Rapid Characterization of Biomolecular Structure and Dynamics
Computations are extensively used for investigating sequence-structure-function relations in proteins. Some recent applications of computational methods for characterizing the structure and dynamics of biomolecules will be presented. Four approaches will be emphasized: (i) the use of singular value decomposition technique for structural classification, - in particular the determination of proteins' structural classes based on their amino acid composition, or the classification of potential anticancer drugs based on their tumor growth inhibitory activities, (ii) database extraction of residue-specific empirical potentials and secondary structure propensities, (iii) coarse-grained simulations of proteins using low resolution models and empirical force fields, and (iv) estimation of functional motions of proteins or their complexes using a Gaussian network model representation of the three-dimensional structure, and a decomposition of thermal fluctuations into a collection of normal modes. The utility and limitations of these approaches will be discussed with illustrative examples.