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首页> 外文期刊>The Journal of Chemical Physics >All-atom calculation of protein free-energy profiles
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All-atom calculation of protein free-energy profiles

机译：全原子计算蛋白质自由能谱

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摘要

The Bias Functional (BF) approach is a variational method which enables one to efficiently generate ensembles of reactive trajectories for complex biomolecular transitions, using ordinary computer clusters. For example, this scheme was applied to simulate in atomistic detail the folding of proteins consisting of several hundreds of amino acids and with experimental folding time of several minutes. A drawback of the BF approach is that it produces trajectories which do not satisfy microscopic reversibility. Consequently, this method cannot be used to directly compute equilibrium observables, such as free energy landscapes or equilibrium constants. In this work, we develop a statistical analysis which permits us to compute the potential of mean-force (PMF) along an arbitrary collective coordinate, by exploiting the information contained in the reactive trajectories calculated with the BF approach. We assess the accuracy and computational efficiency of this scheme by comparing its results with the PMF obtained for a small protein by means of plain molecular dynamics. Published by AIP Publishing.
机译：偏置函数（BF）方法是一种变分方法，其使得能够使用普通计算机集群来有效地产生复杂的生物分子转换的反应轨迹的整合。例如，该方案用于模拟原子细节，蛋白质的折叠由几百个氨基酸组成，并且具有几分钟的实验折叠时间。 BF方法的缺点是它产生不满足显微可逆性的轨迹。因此，该方法不能用于直接计算平衡可观察到，例如自由能景观或平衡常数。在这项工作中，我们开发了一个统计分析，其允许我们通过利用由BF方法计算的反应轨迹中包含的信息来计算沿任意集体坐标的平均力（PMF）的电位。通过将其结果与通过普通分子动力学的普通分子动力学进行比较，通过将其结果与小蛋白质获得的PMF进行比较来评估该方案的准确性和计算效率。通过AIP发布发布。

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