Changhao Wang

TL;DR: The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits, and recent applications in various important biomedical and chemical fields are reviewed.

TL;DR: Upon correction of the binding‐induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods.

TL;DR: A second-order finite-difference numerical method to solve the widely used Poisson-Boltzmann equation for electrostatic analyses of realistic bio-molecules is explored and found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface.

TL;DR: In this article, the authors provide a thorough review of published efforts to adapt the numerical Poisson-Boltzmann methods to molecular simulations so that these methods can be extended to biomolecular studies involving conformational fluctuation and/or dynamics.

TL;DR: This study explored and evaluated a strategy based on the "induced surface charge" to eliminate the dielectric jump within the finite-difference discretization scheme and showed that the strategy is consistent with theory and the classical finite-Difference method on the tested systems.