Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

Nov 13, Tue 2007
11:00 am, MRB 200 Conference Room

Dr. Nathan Baker

Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis

Assessing the performance of Poisson-Boltzmann continuum solvation models

Continuum electrostatics methods have become increasingly popular due to their ability to provide approximate descriptions of salvation energies and forces without expensive sampling required by explicit solvent models. In particular, the Poisson-Boltzmann equation (PBE) provides electrostatic potentials, solvation energies, and forces by modeling the solvent as a featureless, dielectric material, and the mobile ions as a continuous distribution of charge.  In this talk, I will provide a review of PBE-based a new apolar continuum salvation methods as well as approaches for assessing their performance by comparison with explicit solvent simulations.  In particular, I will focus on the ability of these continuum solvent models to describe solvation forces on proteins and nucleic acids and will comment briefly on the extension of such methods to biomembrane systems.