SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules

Abstract

In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many typical calculations, including the molecular surface, electrostatic potential, solvation free energy, entropy, and binding free energy. Among all of the calculations, the entropy calculation is the most timeconsuming one. In SurfPB, the calculation can be performed in a vacuum or implicit solvent and accelerated on GPU. The Poisson−Boltzmann equation solver is accelerated on GPU as well. Moreover, we developed a graphical user interface for SurfPB. It allows users to input the parameters and complete the whole calculation in a visual way. The calculated electrostatic potentials are shown on the molecular surface in a three-dimensional scene.