Effective Born radii in the generalized Born approximation: The importance of being perfect
Effective Born radii in the generalized Born approximation: The importance of being perfect
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DOI：
10.1002/jcc.10126
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发表时间：
2002-11-15
影响因子：
3
通讯作者：
Bashford, D
中科院分区：
文献类型：
--
作者：
Onufriev, A;Case, DA;Bashford, D
广义玻恩（GB）模型提供了，在许多应用中，一个准确的和计算方便的估计静电的贡献水溶剂化。GB模型涉及两种主要类型的近似相对于泊松方程（PE）理论，他们是基于。首先，估计了单个原子的自能贡献，并表示为“有效玻恩半径”。“接下来，原子对的贡献由分析函数f（GB）估计，该函数取决于原子对的有效玻恩半径和原子间距离。在这里，这些近似的相对影响进行了研究，通过计算“完美”的有效玻恩半径从PE理论，并询问如何以及原子成对的能量项从GB模型使用这些完美的半径在标准的f（GB）函数复制从PE理论的等效条款。在对几种生物大分子的测试中，这些完美半径的使用大大提高了原子对项的准确性;也就是说，f（GB）的标准形式表现得相当好。剩余的小误差具有系统和随机分量。如果不显著增加GB模型的复杂性，则不能去除后者，但是f（GB）的替代选择可以减少系统部分。使用完美半径GB模型的分子动力学模拟与使用常规GB的模拟相比毫不逊色，即使在前者的半径保持固定。这些结果量化，为GB字段，得到有效玻恩半径的权利的重要性，事实上，完美的半径，GB模型给出了一个非常好的近似的各种生物大分子类型和构象的基本PE理论。(C)2002 Wiley Periodicals，Inc.
Generalized Born (GB) models provide, for many applications, an accurate and computationally facile estimate of the electrostatic contribution to aqueous solvation. The GB models involve two main types of approximations relative to the Poisson equation (PE) theory on which they are based. First, the self-energy contributions of individual atoms are estimated and expressed as "effective Born radii." Next, the atom-pair contributions are estimated by an analytical function f(GB) that depends upon the effective Born radii and interatomic distance of the atom pairs. Here, the relative impacts of these approximations are investigated by calculating "perfect" effective Born radii from PE theory, and enquiring as to how well the atom-pairwise energy terms from a GB model using these perfect radii in the standard f(GB) function duplicate the equivalent terms from PE theory. In tests on several biological macromolecules, the use of these perfect radii greatly increases the accuracy of the atom-pair terms; that is, the standard form of f(GB) performs quite well. The remaining small error has a systematic and a random component. The latter cannot be removed without significantly increasing the complexity of the GB model, but an alternative choice of f(GB) can reduce the systematic part. A molecular dynamics simulation using a perfect-radii GB model compares favorably with simulations using conventional GB, even though the radii remain fixed in the former. These results quantify, for the GB field, the importance of getting the effective Born radii right; indeed, with perfect radii, the GB model gives a very good approximation to the underlying PE theory for a variety of biomacromolecular types and conformations. (C) 2002 Wiley Periodicals, Inc.