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Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies
Author(s) -
Nguyen Duc D.,
Wang Bao,
Wei GuoWei
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24757
Subject(s) - solvation , poisson–boltzmann equation , grid , solvent models , computation , work (physics) , statistical physics , binding energy , solver , electrostatics , implicit solvation , approximation error , chemistry , boltzmann constant , molecule , computational chemistry , computational physics , computer science , physics , algorithm , thermodynamics , atomic physics , mathematics , mathematical optimization , ion , organic chemistry , geometry
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, Δ G el, and binding free energy, Δ Δ G el, 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 Δ G elobtained at the grid spacing of 1.0 Å compared to Δ G elat 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 Δ Δ G elcalculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc.