The AGBNP2 Implicit Solvation Model.
The AGBNP2 Implicit Solvation Model.
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DOI：
10.1021/ct900234u
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发表时间：
2009-07-31
影响因子：
5.5
通讯作者：
Levy, Ronald M.
中科院分区：
文献类型：
--
作者：
Gallicchio, Emilio;Paris, Kristina;Levy, Ronald M.
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。引入了一种新的经验水合自由能分量，该分量基于在溶质表面定位和评分水合位点的程序，以模拟连续介质模型描述不佳的第一溶剂化壳效应，例如氢键合。这个新的分量被添加到广义玻恩和非极性AGBNP项中。还新引入的是一个分析溶剂排除体积（SEV）模型，它提高了溶质体积的描述，通过减少传统的货车德瓦尔斯表示中存在的虚假的高介电间隙空间的影响。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。结果表明，新的体积模型产生的玻恩半径和表面积与这些数量的精确数值评价吻合良好。一系列的迷你蛋白质的分子动力学模拟的结果表明，新的模型产生的构象合奏在实质上更好的协议与参考明确的溶剂合奏比原来的AGBNP模型的结构和能量的措施。
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 terms. Also newly introduced is an analytical Solvent Excluded Volume (SEV) model which improves the solute volume description by reducing the effect of spurious high-dielectric interstitial spaces present in conventional van der Waals representations. 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. It is shown that the new volumetric model produces Born radii and surface areas in good agreement with accurate numerical evaluations of these quantities. 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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影响因子：
56.9
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
5.5
作者：
Felts, Anthony K.;Gallicchio, Emilio;Levy, Ronald M.
通讯作者：
Levy, Ronald M.
影响因子：
2.9
作者：
Felts, AK;Harano, Y;Levy, RM
通讯作者：
Levy, RM
影响因子：
3
作者：
Chocholousova, J;Feig, M
通讯作者：
Feig, M
DOI：
10.1073/pnas.0408970102
发表时间：
2005-05-10
影响因子：
11.1
作者：
Andrec, M;Felts, AK;Levy, RM
通讯作者：
Levy, RM