ATOMIC SOLVATION PARAMETERS IN THE ANALYSIS OF PROTEIN-PROTEIN DOCKING RESULTS
ATOMIC SOLVATION PARAMETERS IN THE ANALYSIS OF PROTEIN-PROTEIN DOCKING RESULTS
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DOI：
10.1002/pro.5560041014
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发表时间：
1995-10-01
期刊：
影响因子：
8
通讯作者：
READ, RJ
中科院分区：
文献类型：
--
作者：
CUMMINGS, MD;HART, TN;READ, RJ
几套氨基酸的表面积和转移自由能被用来推导出总共九套原子溶剂化参数（ASP）。我们测试了这些参数的准确性，在预测的实验确定的氨基酸衍生物的参数推导出的转移自由能。在所有情况下，计算值和实验值相关性良好。然后，我们选择了三个参数集，并研究了添加一个充满活力的校正去溶剂化的基础上，这三个参数集，我们的多个启动蒙特卡罗对接方法中使用的简单的潜在功能的效果。各种蛋白质-蛋白质相互作用和对接的结果进行了检查。在研究的对接模拟中，去溶剂化校正仅在每次模拟的最终能量计算期间应用。对于大多数的对接结果，我们分析，使用的辛醇-水为基础的ASP集略有改善的精力充沛的排名的低能量对接，而其他ASP集，我们测试扰乱了排名的低能量对接在许多相同的系统。我们还研究了一系列蛋白酶抑制剂复合物的实验自由能协会和我们计算的相互作用能之间的相关性。同样，基于辛醇-水的ASP集与我们的标准电位函数兼容，而来自其他溶剂系统的ASP集则不兼容。
Several sets of amino acid surface areas and transfer free energies were used to derive a total of nine sets of atomic solvation parameters (ASPs). We tested the accuracy of each of these sets of parameters in predicting the experimentally determined transfer free energies of the amino acid derivatives from which the parameters were derived. In all cases, the calculated and experimental values correlated well. We then chose three parameter sets and examined the effect of adding an energetic correction for desolvation based on these three parameter sets to the simple potential function used in our multiple start Monte Carlo docking method. A variety of protein-protein interactions and docking results were examined. In the docking simulations studied, the desolvation correction was only applied during the final energy calculation of each simulation. For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed the ranking of the low-energy dockings in many of the same systems. We also examined the correlation between the experimental free energies of association and our calculated interaction energies for a series of proteinase-inhibitor complexes. Again, the octanol-water-based ASP set was compatible with our standard potential function, whereas ASP sets derived from other solvent systems were not.