Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies

Duc D. Nguyen, Bao Wang, Guo Wei Wei

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

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, ∆Gel, and binding free energy, ∆∆Gel, 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 ∆Gel obtained at the grid spacing of 1.0 Å compared to ∆Gel 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 ∆Gel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening.

Original languageEnglish
Pages (from-to)941-948
Number of pages8
JournalJournal of Computational Chemistry
Volume38
Issue number13
DOIs
StatePublished - May 15 2017

Bibliographical note

Publisher Copyright:
© 2017 Wiley Periodicals, Inc.

Keywords

  • accurate coarse grid Poisson–Boltzmann solver
  • electrostatic binding free energy
  • reaction field energy

ASJC Scopus subject areas

  • General Chemistry
  • Computational Mathematics

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