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

Published: 28-11-2019| Version 1 | DOI: 10.17632/d77n7yskmc.1
Ján Buša Jr.,
Ján Buša,
Edik Hayryan,
Shura Hayryan,
Chin-Kun Hu,
Imrich Pokorný,
Jaroslav Skřivánek


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.