U.S.-France Cooperative Research: Implicit Solvent Models for Biomolecular Simulations

The Scripps Research Institute, La Jolla CA

Investigators

Abstract

0128783 Case This three-year award for U.S.-France collaboration in computational biophysics involves researchers at the Scripps Research Institute and the Institute for Molecular and Cellular Biology and Genetics in Strasbourg, France. David A. Case, Charles L. Brooks III in the US and Thomas Simonson in France lead the collaborative program. The joint effort is aimed at the development and distribution of computer codes for molecular dynamics simulations of proteins and nucleic acids. The specific aims include performance of critical tests for parameterizations and implementation of the generalized Born solvent model and new applications for NMR (Nuclear Magnetic Resonance) structure refinement and for behavior of biomolecules. The investigators have complementary expertise in biomolecular simulation and in widely used computer programs: CNS/XPLOR (Simonson), CHARMM (Brooks) and AMBER (Case). The new distributed computer codes will allow new types of biomolecular simulations. The enhanced generalized Born model will be used for structure prediction, prediction of protein-ligand interactions, protein folding, structure-function analyses. This award represents the US side of parallel proposals to the NSF and the French National Center for Scientific Research (CNRS). NSF will cover travel funds and living expenses of the US investigators and graduate students. The CNRS will support visits to the US by the French participants. The project adds an international dimension to research training of graduate students and enhances opportunities for future collaborative partnerships.