Jeffry Madura
Biomolecular Simulations
Friday, November 21, 2008, 11:00am
6014 Biomedical Science Tower 3 (University of Pittsburgh)
Joint CMU-PItt Ph.D. Program in Computational Biology Lecture Series
Refreshments will be served.
Abstract: There are a variety of computational methods, e.g. continuum electrostatics, molecular dynamics, Brownian dynamics, free energy perturbation, principal component analysis, comparative modeling, and anisotropic network model that are available to model biomolecular structures. We have used most of these methods as well as combinations of these methods to study the effect of non-nucleoside binding substrates on HIV-RT dynamics, the interaction of proteins at ice/water interfaces, diffusion of nanoclusters to and on surfaces, and calculating bimolecular diffusion-controlled rate constants. Most recently we have been using molecular dynamics to study peptide stability in salt solutions and using continuum electrostatic methods to study the binding of antidepressants to neurotransporters. I will present the results from our current efforts in these areas.