Improving the description of salt bridge strength and geometry in a Generalized Born model.
Improving the description of salt bridge strength and geometry in a Generalized Born model.
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DOI：
10.1016/j.jmgm.2010.11.013
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发表时间：
2011-02
影响因子：
2.9
通讯作者：
Simmerling, Carlos
中科院分区：
文献类型：
--
作者：
Shang, Yi;Nguyen, Hai;Wickstrom, Lauren;Okur, Asim;Simmerling, Carlos
广义玻恩（GB）溶剂模型被广泛用于分子动力学模拟，因为它可以更便宜的计算成本，它的样品构象变化更有效地比显式溶剂模拟。与此同时，在过去已经做出了很大的努力来提高其精度和准确性。以往的研究表明，降低某些氢原子的本征GB半径可以提高AMBERGB-HCT溶剂模型对盐桥的准确性。在这里，我们提出了我们的发现，类似的校正也显示了显着的改善，为琥珀GB-OBC溶剂模型。小肽复制交换分子动力学模拟的平均力和聚类分析的潜力表明，新半径GB模拟与ff 99 SB/GB-OBC校正盐桥强度，并实现了显着更高的几何相似性与TIP 3 P模拟。在60 ns HIV-1蛋白酶GB模拟中的改进性能进一步验证了这种方法用于大型系统。
The Generalized Born (GB) solvent model is widely used in molecular dynamics simulations because it can be less computationally expensive and it samples conformational changes more efficiently than explicit solvent simulations. Meanwhile, great efforts have been made in the past to improve its precision and accuracy. Previous studies have shown that reducing intrinsic GB radii of some hydrogen atoms would improve AMBER GB-HCT solvent model's accuracy on salt bridges. Here we present our finding that similar correction also shows dramatic improvement for the AMBER GB-OBC solvent model. Potential of mean force and cluster analysis for small peptide replica exchange molecular dynamics simulations suggested that new radii GB simulation with ff99SB/GB-OBC corrected salt bridge strength and achieved significantly higher geometry similarity with TIP3P simulation. Improved performance in 60 ns HIV-1 protease GB simulation further validated this approach for large systems.
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影响因子：
15
作者：
Amaro RE;Cheng X;Ivanov I;Xu D;McCammon JA
通讯作者：
McCammon JA
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：
15
作者：
Galiano, Luis;Ding, Fangyu;Fanucci, Gail E.
通讯作者：
Fanucci, Gail E.
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
--
作者：
BONDI, A
通讯作者：
BONDI, A