Long-timescale molecular dynamics simulations of protein structure and function
Long-timescale molecular dynamics simulations of protein structure and function
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DOI：
10.1016/j.sbi.2009.03.004
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发表时间：
2009-04-01
影响因子：
6.8
通讯作者：
Shaw, David E.
中科院分区：
文献类型：
--
作者：
Klepeis, John L.;Lindorff-Larsen, Kresten;Shaw, David E.
分子动力学模拟允许对生物分子过程进行原子水平的表征，例如与蛋白质功能相关的构象转变。然而，此类模拟的计算需求历来使它们无法达到这些事件经常发生的微秒和更大的时间尺度。在算法、软件和计算机硬件方面的最新进展使得对数万个原子的微秒时间尺度的模拟成为现实，毫秒时间尺度的模拟即将出现。本文概述了这些在高性能分子动力学模拟方面的进展，并讨论了最近在蛋白质动力学和功能研究以及基本计算模型的实验验证中的应用。
Molecular dynamics simulations allow for atomic-level characterization of biomolecular processes such as the conformational transitions associated with protein function. The computational demands of such simulations, however, have historically prevented them from reaching the microsecond and greater timescales on which these events often occur. Recent advances in algorithms, software, and computer hardware have made microsecond-timescale simulations with tens of thousands of atoms practical, with millisecond-timescale simulations on the horizon. This review outlines these advances in high-performance molecular dynamics simulation and discusses recent applications to studies of protein dynamics and function as well as experimental validation of the underlying computational models.