D. E. Shaw Research, New York, NY 10036, USA.
D. E. Shaw Research, New York, NY 10036, USA.
Curr Opin Struct Biol. 2014 Feb;24:98-105. doi: 10.1016/j.sbi.2013.12.006. Epub 2014 Jan 24.
Advances in computer hardware, software and algorithms have now made it possible to run atomistically detailed, physics-based molecular dynamics simulations of sufficient length to observe multiple instances of protein folding and unfolding within a single equilibrium trajectory. Although such studies have already begun to provide new insights into the process of protein folding, realizing the full potential of this approach will depend not only on simulation speed, but on the accuracy of the physical models ('force fields') on which such simulations are based. While experimental data are not available for comparison with all of the salient characteristics observable in long protein-folding simulations, we examine here the extent to which current force fields reproduce (and fail to reproduce) certain relevant properties for which such comparisons are possible.
计算机硬件、软件和算法的进步使得人们现在有可能运行原子细节、基于物理的分子动力学模拟，其长度足以在单个平衡轨迹中观察到多个蛋白质折叠和展开的实例。虽然这些研究已经开始为蛋白质折叠过程提供新的见解，但要充分发挥这种方法的潜力，不仅取决于模拟速度，还取决于此类模拟所基于的物理模型（“力场”）的准确性。虽然没有实验数据可与长蛋白质折叠模拟中可观察到的所有显著特征进行比较，但我们在这里研究了当前力场在多大程度上再现（和未能再现）某些相关性质，这些性质的比较是可能的。
