Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.

ABSTRACT: The efficient and accurate characterization of solvent effects is a key element in the theoretical and computational study of biological problems. Implicit solvent models, particularly generalized Born (GB) continuum electrostatics, have emerged as an attractive tool to study the structure and dynamics of biomolecules in various environments. Despite recent advances in this methodology, there remain limitations in the parametrization of many of these models. In the present work, we demonstrate that it is possible to achieve a balanced implicit solvent force field by further optimizing the input atomic radii in combination with adjusting the protein backbone torsional energetics. This parameter optimization is guided by the potentials of mean force (PMFs) between amino acid polar groups, ca

SUBMITTER: Chen J 

PROVIDER: S-EPMC2596729 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature