New analytic approximation to the standard molecular volume definition and its application to generalized born calculations
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations
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DOI：
10.1002/jcc.10272
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发表时间：
2003-08-01
影响因子：
3
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Lee, MS;Feig, M;Brooks, CL
在最近的一篇文章(Lee，M.S.；Salsbury，F.R.Jr.；Brooks，C.L.，III.J Chem Phys2002,116,10606)中，我们证明了如果使用相同的分子体积定义，广义Born(GB)理论提供了一个很好的近似泊松静电溶剂化能计算的方法。在这项工作中，我们提出了一种新的和改进的解析方法来再现Lee-Richards分子体积，这是泊松计算中最常见的体积定义。总体而言，对于大量蛋白质的绝对溶剂化能和蛋白质构象的相对溶剂化能，误差为1%。我们还引入了一种精确的SASA近似，它使用与我们的GB方法相同的机制，并且需要少量的计算成本。结合的方法被证明产生了一个有效和准确的隐式溶剂表示法来模拟生物聚合物。(C)2003年威利期刊公司。
In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee-Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers. (C) 2003 Wiley Periodicals, Inc.