Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

ABSTRACT: Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG_pol) and binding free energies (ΔΔG_pol). The model tolerates a relatively coarse gri

SUBMITTER: Forouzesh N 

PROVIDER: S-EPMC12085165 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature