An accelerated nonlocal Poisson-Boltzmann equation solver for electrostatics of biomolecule

International Journal for Numerical Methods in Biomedical Engineering
Jinyong Ying, Dexuan Xie

Abstract

The nonlocal modified Poisson-Boltzmann equation (NMPBE) is one important variant of a commonly used dielectric continuum model, the Poisson-Boltzmann equation (PBE), for computing electrostatics of biomolecules. In this paper, an accelerated NMPBE solver is constructed by finite element and finite difference hybrid techniques. It is then programmed as a software package for computing electrostatic solvation and binding free energies for a protein in a symmetric 1:1 ionic solvent. Numerical results validate the new solver and its numerical stability. They also demonstrate that the new solver has much better performance than the corresponding finite element solver in terms of computer CPU time. Furthermore, they show that the binding free energies produced by NMPBE can match chemical experiment data better than those by PBE.

References

Dec 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·K J BreslauerL A Marky
Sep 28, 2004·Physical Review Letters·A HildebrandtH-P Lenhof
Mar 14, 2008·Journal of Molecular Graphics & Modelling·Zeyun YuJ Andrew McCammon
Aug 5, 2010·Biophysical Journal·Marcia O FenleyAlexander H Boschitsch
Sep 3, 2013·Journal of Chemical Theory and Computation·Robert C HarrisMarcia O Fenley

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Citations

Oct 31, 2021·International Journal for Numerical Methods in Biomedical Engineering·Jiao Li, Jinyong Ying

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