AGBNP2隐式溶剂化模型
The AGBNP2 Implicit Solvation Model
摘要：
AGBNP 2隐式溶剂模型，分析广义玻恩加非极性（AGBNP）模型，我们以前报道的演变，提出了与建模超出传统的连续介质介电表示所描述的水合作用的目的。一个新的经验水化自由能组件的基础上的程序来定位和评分溶质表面上的水化位点的模型第一溶剂化壳效应，如氢键，这是很差的连续介质模型描述。这个新的组件被添加到广义玻恩和非极性AGBNP模型，已得到改进的溶质体积描述的描述。我们已经介绍了一种分析溶剂排除体积（SEV）模型，它减少了虚假的高介电间隙空间中存在的传统的范德华表示的溶质体积的影响。AGBNP 2模型的参数化和测试相对于实验水合自由能的小分子和显式溶剂模拟的结果。对水的粒度进行建模是第一壳溶剂化函数和SEV模型所采用的主要设计原理之一，这是通过要求水位置具有基于水分子大小的最小可用体积来实现的。我们表明，新的体积模型产生的玻恩半径和表面积与准确的数值计算吻合得很好。分子动力学模拟的一系列迷你蛋白质的结果表明，新的模型产生的构象系综在实质上更好的协议与参考明确的溶剂系综比原来的AGBNP模型的结构和能量的措施。
英文摘要：
The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional continuum dielectric representations. A new empirical hydration free energy component based on a procedure to locate and score hydration sites on the solute surface is introduced to model first solvation shell effects, such as hydrogen bonding, which are poorly described by continuum dielectric models. This new component is added to the Generalized Born and non-polar AGBNP models which have been improved with respect to the description of the solute volume description. We have introduced an analytical Solvent Excluding Volume (SEV) model which reduces the effect of spurious high-dielectric interstitial spaces present in conventional van der Waals representations of the solute volume. The AGBNP2 model is parametrized and tested with respect to experimental hydration free energies of small molecules and the results of explicit solvent simulations. Modeling the granularity of water is one of the main design principles employed for the the first shell solvation function and the SEV model, by requiring that water locations have a minimum available volume based on the size of a water molecule. We show that the new volumetric model produces Born radii and surface areas in good agreement with accurate numerical evaluations. The results of Molecular Dynamics simulations of a series of mini-proteins show that the new model produces conformational ensembles in substantially better agreement with reference explicit solvent ensembles than the original AGBNP model with respect to both structural and energetics measures.
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