Parameterization and application of an implicit solvent model for macromolecules

As the field of theoretical biophysics begins to recognize systems of longe r timescales and larger magnitude, rapid approaches for investigating these systems are required. One promising simplification of the typical system o f a solute surrounded by water is the use of implicit solvation models. The generalized Born implicit solvent offers a rapid approach For computing th e electrostatic effects of bulk solvent without the explicit representation of water molecules. This report describes the parameterization of a genera lized Born (GB) model for protein and nucleic acid structures. As a demonst ration of the usefulness of this approach, the GB model is applied toward t he discrimination of misfolded and properly folded protein structures. This study attempts to illustrate the potential of the GB model for molecular d ynamics simulations over longer timescales as well as for screening large s tructural databases.