title: Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.
abstract: Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Mathematics, Michigan State University, Michigan, 48824.
authors.forename: Duc D
authors.initials: DD
authors.lastname: Nguyen
authors.affiliation: Department of Mathematics, Michigan State University, Michigan, 48824.
authors.forename: Bao
authors.initials: B
authors.lastname: Wang
authors.affiliation: Department of Mathematics, Michigan State University, Michigan, 48824.|Department of Electrical and Computer Engineering, Michigan State University, Michigan, 48824.|Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, 48824.
authors.forename: Guo-Wei
authors.identifier: 0000-0002-5781-2937
authors.initials: GW
authors.lastname: Wei
mesh_terms: D039301:Computers, Molecular; D008958:Models, Molecular; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D012997:Solvents
keywords: accurate coarse grid Poisson-Boltzmann solver; electrostatic binding free energy; reaction field energy