精确、稳健和可靠的泊松-玻尔绑定能量计算
Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies
AI总结：
本文研究了在不同网格间距下MIBPB求解器对静电溶化自由能和静电绑定自由能的计算精度，发现0.6 Å网格间距可保证计算的准确性和可靠性，1.1 Å网格间距适合高通量筛选。
摘要：
泊松-玻尔模型是生物物理建模和计算中最受欢迎的隐式溶剂模型之一。提供准确且可靠的泊松-玻尔估计静电溶化自由能ΔG_el和绑定自由能ΔΔG_el的能力对计算生物物理和生物化学具有重要意义。最近文献（《化学理论计算杂志》2013，9，3677-3685）警告，广泛使用的0.5 Å网格间距在计算溶剂排除表面（SES）下的ΔΔG_el时会产生不可接受的误差。在本工作中，我们研究了我们的PB求解器（MIBPB）在使用SESs时对静电溶化自由能和静电绑定自由能的网格依赖性。发现相对于0.2 Å网格间距下的ΔG_el，1.0 Å网格间距下153种分子的平均相对绝对误差小于0.2%。我们的结果表明，使用0.6 Å网格间距可确保ΔΔG_el计算的准确性和可靠性。事实上，1.1 Å网格间距似乎在高通量筛选中提供了足够的准确性。
英文摘要：
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, $ΔG_{\text{el}}$, and binding free energy, $ΔΔG_{\text{el}}$, 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 $0.5$ Å$ $ produces unacceptable errors in $ΔΔG_{\text{el}}$ 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 $ΔG_{\text{el}}$ obtained at the grid spacing of $1.0$ Å$ $ compared to $ΔG_{\text{el}}$ 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 $ΔΔG_{\text{el}}$ calculation. In fact, the grid spacing of $1.1$ Å$ $ appears to deliver adequate accuracy for high throughput screening.
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