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

Duc D. Nguyen, Bao Wang, Guo Wei Wei

    Research output: Contribution to journalArticle

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

    Profile

    Ludwig Boltzmann
    Free energy
    Siméon Denis Poisson
    Grid
    Hemerythrin
    Binding energy
    Electrostatics
    Spacing
    Community Psychiatry
    Model
    Cystaphos
    Anthralin
    Solvation
    Biophysics
    High-throughput screening
    Biochemistry
    Molecules
    Modeling
    Edema Disease of Swine
    Cardiotonic Agents

    Keywords

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

    ASJC Scopus subject areas

    • Chemistry(all)
    • Computational Mathematics

    Cite this

    Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies. / Nguyen, Duc D.; Wang, Bao; Wei, Guo Wei.

    In: Journal of Computational Chemistry, Vol. 38, No. 13, 15.05.2017, p. 941-948.

    Research output: Contribution to journalArticle

    Nguyen, Duc D.; Wang, Bao; Wei, Guo Wei / Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies.

    In: Journal of Computational Chemistry, Vol. 38, No. 13, 15.05.2017, p. 941-948.

    Research output: Contribution to journalArticle

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