PBCAVE: Program for exact classification of the mesh points of a protein with possible internal cavities and its application to Poisson-Boltzmann equation solution

摘要

The main contribution of the program is in the analytic approach to the setting of dielectric constant for all discretization points of a grid in the computational domain according to their locations with respect to the molecular surface allowing also taking into account possible cavities. Assigned values of dielectric constant are used in a solver of the linear Poisson-Boltzmann equation for a protein-water system using a finite difference method. (C) 2019 Elsevier B.V. All rights reserved.