A revised density function for molecular surface definition in continuum solvent models.
A revised density function for molecular surface definition in continuum solvent models.
复制标题
连续溶剂模型中分子表面定义的修订密度函数。
DOI：
10.1021/ct900318u
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发表时间：
2010
影响因子：
5.5
通讯作者：
Luo,Ray
中科院分区：
文献类型：
--
作者：
Ye,Xiang;Wang,Jun;Luo,Ray
为了获得更好的收敛性和更高的数值稳定性，开发了一个修正的密度函数来定义数值泊松-玻尔兹曼方法的分子表面。新的密度函数不使用任何预定义的函数形式，而是通过数值优化来再现用溶剂排除表面定义计算的反应场能。优化中使用了参数空间的穷举搜索，使用了广泛的训练分子，包括蛋白质、核酸和折叠和未折叠构象的肽。为了保证密度函数具有良好的数值性能，引入了三次样条函数。实验结果表明，对于不同大小和构象的训练分子和测试分子，用修正密度函数计算的平均相对能量误差均小于1%。我们的可转移性分析表明，新方法的性能在很大程度上与尺寸和构象无关。详细的分析进一步表明，用修正的密度函数计算的数值力相对于网格间距收敛得更好，并且在测试的肽中数值上更稳定。
A revised density function is developed to define the molecular surface for the numerical Poisson−Boltzmann methods to achieve a better convergence and a higher numerical stability. The new density function does not use any predefined functional form but is numerically optimized to reproduce the reaction field energies computed with the solvent excluded surface definition. An exhaustive search in the parameter space is utilized in the optimization, using a wide-range of training molecules including proteins, nucleic acids, and peptides in both folded and unfolded conformations. A cubic-spline function is introduced to guarantee good numerical behavior of the new density function. Our test results show that the average relative energy errors computed with the revised density function are uniformly lower than 1% for both training and test molecules with different sizes and conformations. Our transferability analysis shows that the performance of the new method is mostly size and conformation independent. A detailed analysis further shows that the numerical forces computed with the revised density function converge better with respect to the grid spacing and are numerically more stable in tested peptides.