@Article{CiCP-23-520,
author = {Jingzhen Hu, Shan Zhao and Weihua Geng},
title = {Accurate p$K_a$ Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver},
journal = {Communications in Computational Physics},
year = {2018},
volume = {23},
number = {2},
pages = {520--539},
abstract = {<p style="text-align: justify;">The <span style="text-align: justify;">p$K_a$</span> values are important quantities characterizing the ability of protein
active sites to give up protons. p$K_a$ can be measured using NMR by tracing chemical-shifts
of some special atoms, which is however expensive and time-consuming. Alternatively,&nbsp;<span style="text-align: justify;">p$K_a$</span> can be calculated numerically by electrostatic free energy changes subject
to the protonation and deprotonation of titration sites. To this end, the Poisson-Boltzmann
(PB) model is an effective approach for the electrostatics. However, numerically
solving PB equation is challenging due to the jump conditions across the
dielectric interfaces, irregular geometry of the molecular surface, and charge singularities.
Our recently developed matched interface and boundary (MIB) method treats
these challenges rigorously, resulting in a solid second order MIBPB solver. Since the
MIBPB solver uses Green&#39;s function based regularization of charge singularities by decomposing
the solution into a singular component and a regularized component, it
is particularly efficient in treating the accuracy-sensitive, numerous, and complicated
charge distributions from the <span style="text-align: justify;">p$K_a$</span> calculation. Our numerical results demonstrate that
accurate free energies and <span style="text-align: justify;">p$K_a$</span> values are achieved at coarse grid rapidly. In addition,
the resulting software, which pipelines the entire <span style="text-align: justify;">p$K_a$</span> calculation procedure, is
available to all potential users from the greater bioscience community.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.OA-2017-0078},
url = {http://global-sci.org/intro/article_detail/cicp/10536.html}
}