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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Comparative study of generalized Born models: Protein dynamics
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Comparative study of generalized Born models: Protein dynamics

机译：广义Born模型的比较研究：蛋白质动力学

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摘要

In this work, we compare the results of molecular dynamics simulations involving the application of three generalized Born (GB) models to 10 different proteins. The three GB models, the Still, HCT, and modified analytical generalized Born models, were implemented in the computationally efficient GROMACS package. The performance of each model was assessed from the backbone rms deviation from the native structure, the number of native hydrogen bonds retained in the simulation, and the experimental and calculated radius of gyration. Analysis of variance (ANOVA) was used to analyze the results of the simulations. The rms deviation measure was found to be unable to distinguish the quality of the results obtained with the three different GB models, whereas the number of native hydrogen bonds and radius of gyration yielded a statistically meaningful discrimination among models. Our results suggest that, of the three, modified analytical generalized Born yields the best agreement between calculated and experimentally derived structures. More generally, our study highlights the need both to evaluate the effects of different variables on the results of simulations and to verify that the results of molecular dynamics simulations are statistically meaningful.
机译：在这项工作中，我们比较了分子动力学模拟的结果，这些结果涉及将三个广义Born（GB）模型应用于10种不同的蛋白质。三种GB模型（Still，HCT和修改后的解析广义Born模型）已在高效计算的GROMACS软件包中实现。根据主链均方根与天然结构的偏差，模拟中保留的天然氢键的数量以及实验和计算的回转半径来评估每个模型的性能。方差分析（ANOVA）用于分析模拟结果。发现均方根偏差度量无法区分使用三种不同GB模型获得的结果的质量，而天然氢键的数量和回转半径在模型之间产生了具有统计学意义的区别。我们的结果表明，在这三种改良的分析广义Born中，计算得出的结构和实验得出的结构之间的一致性最佳。更广泛地说，我们的研究强调了既需要评估不同变量对模拟结果的影响，又需要验证分子动力学模拟的结果在统计上是否有意义。

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