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A fast and accurate analytical method for the computation of solvent effects in molecular simulations.

机译：一种在分子模拟中计算溶剂效应的快速准确的分析方法。

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The solvent environment of molecules plays a very important role in their structure and function. In biological systems it is well known that water has profound effects in the functions of proteins. Simulations assist us in microscopic studies of chemical and biological phenomena. It is important then to include solvation effects accurately and efficiently in molecular simulations. In this work we present a novel approximate analytical method for calculating the solvation energy for every atom of a molecular system and the forces that act on each atom because of the solvent. The solvation energy is partitioned into long-range and short-range contributions. The long-range contributions are due to polar interactions between the solvent and the solute and the short-range are due to van der Waals and entropic effects. We show how the calculation of these effects, under certain approximations, can be reduced to the calculation of the volume and exposed area of each atom, assuming a fused-sphere model for the solute. We demonstrate a fast method for the exact, analytical calculation of the volume and area of each atom in the fused-sphere model and their gradients with respect to the atom's position. We incorporate the fast geometric algorithms into the approximate formulas we derived for the calculation of the solvation energy, to get our solvation model, the Analytical Volume Generalized Born - Solvent Accessible Surface (AVGB-SAS) model.; The predictions of the polar part of the method (AVGB) are very good as compared to numerical solutions of the underlying physical model, the Poisson-Boltzman equation, for small and large molecular systems. AVGB does not depend on any fitting parameters, which is common in the literature for such approximate methods. It is very fast compared to numerical solutions of the PB equation or other Generalized Born methods. Also, the method is parallelizable which allows us to study much larger systems. The AVGB-SAS method has been implemented in a parallel molecular dynamics software package and a molecular docking software package. We have demonstrated the quality of the results of the AVGB-SAS model in the dynamics of DNA and in rational drug design applications.
机译：分子的溶剂环境在其结构和功能中起着非常重要的作用。在生物系统中，众所周知，水对蛋白质的功能具有深远的影响。模拟有助于我们对化学和生物现象进行微观研究。那么重要的是在分子模拟中准确有效地包括溶剂化作用。在这项工作中，我们提出了一种新颖的近似分析方法，用于计算分子系统中每个原子的溶剂化能以及由于溶剂作用在每个原子上的力。溶剂化能分为远距离和短距离的贡献。远距离的贡献是由于溶剂和溶质之间的极性相互作用，而短距离的贡献是由于范德华力和熵效应。我们展示了如何在假定近似值的情况下，将这些影响的计算简化为每个原子的体积和暴露面积的计算，并假设溶质具有熔融球模型。我们展示了一种快速的方法，用于精确地，解析地计算熔融球体模型中每个原子的体积和面积以及它们相对于原子位置的梯度。我们将快速几何算法合并到为计算溶剂化能而得出的近似公式中，以得到我们的溶剂化模型，即分析体积广义生化-溶剂可及表面（AVGB-SAS）模型。与基础物理模型的数值解决方案（泊松-玻尔兹曼方程）（适用于大小分子系统）的数值解相比，该方法的极性部分（AVGB）的预测非常好。 AVGB不依赖于任何拟合参数，这是此类近似方法在文献中常见的参数。与PB方程的数值解或其他广义的Born方法相比，它非常快。而且，该方法是可并行化的，这使我们能够研究更大的系统。 AVGB-SAS方法已在并行分子动力学软件包和分子对接软件包中实现。我们已经在DNA动力学和合理的药物设计应用中证明了AVGB-SAS模型结果的质量。

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