Past Event: Oden Institute Seminar

Macromolecular simulations using continuum solvent models

David Case, Professor BioMaPS Institute for Quantitative Biology Rutgers University

Abstract

It is often useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. The generalized Born model is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. Strengths and weaknesses will be discussed, both for fidelity to the underlying continuum model, and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations. Two particular recent applications will be emphasized. First, I will discuss the computation of second derivatives of GB energies, using these to generate estimates of entropy and mechanical properties of nucleic acids from an analysis of low-frequency correlated motions. The second topic will look at using short MD simulations to identify good and bad inhibitors in virtual screening analyses of protein-ligand interactions. *Refreshments served at 3:00 pm.