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

Duc D. Nguyen; Bao Wang; Guo-wei Wei

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arXiv · 1603.04054

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

Duc D. Nguyen·Bao Wang·Guo-wei Wei

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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, $\Delta G_{\text{el}}$, and binding free energy, $\Delta\Delta G_{\text{el}}$, is of tremendous significance to computational biophysics and biochemistry. Recently, it has been warned in the literature (Journal of Chemical Theory and Computation 2013, 9, 3677-3685) that the widely used grid spacing of $0.5$ \AA $ $ produces unacceptable errors in $\Delta\Delta G_{\text{el}}$ estimation with the solvent exclude surface (SES). In this work, we investigate the grid dependence of our PB solver (MIBPB) with SESs for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of $\Delta G_{\text{el}}$ obtained at the grid spacing of $1.0$ \AA $ $ compared to $\Delta G_{\text{el}}$ at $0.2$ \AA $ $ averaged over 153 molecules is less than 0.2\%. Our results indicate that the use of grid spacing $0.6$ \AA $ $ ensures accuracy and reliability in $\Delta\Delta G_{\text{el}}$ calculation. In fact, the grid spacing of $1.1$ \AA $ $ appears to deliver adequate accuracy for high throughput screening.

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Duc D. Nguyen, Bao Wang, Guo-wei Wei. 2016-03-13. Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies. https://arxiv.org/abs/1603.04054

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