Escobedo Fernando A, Borrero Ernesto E, Araque Juan C
J Phys Condens Matter. 2009 Aug 19;21(33):333101. doi: 10.1088/0953-8984/21/33/333101. Epub 2009 Jul 13.
The last decade has seen a rapid growth in the number of simulation methods and applications dealing with the sampling of transition pathways of rare nanoscale events. Such studies are crucial, for example, for understanding the mechanism and kinetics of conformational transitions and enzymatic events associated with the function of biomolecules. In this review, a broad account of transition path sampling approaches is provided, starting from the general concepts, progressing to the specific principles that underlie some of the most important methods, and eventually singling out the so-called forward flux sampling method for a more detailed description. This is done because forward flux sampling, despite its appealing simplicity and potential efficiency, has thus far received limited attention from practitioners. While path sampling methods have a widespread application to many types of rare transitional events, here only recent applications involving biomolecules are reviewed, including isomerization, protein folding, and enzyme catalysis.
在过去十年中，处理罕见纳米级事件过渡路径采样的模拟方法和应用数量迅速增长。例如，此类研究对于理解与生物分子功能相关的构象转变和酶促事件的机制及动力学至关重要。在本综述中，我们对过渡路径采样方法进行了广泛介绍，从一般概念入手，进而阐述一些最重要方法所依据的具体原理，最终挑选出所谓的正向通量采样方法进行更详细的描述。之所以这样做，是因为尽管正向通量采样具有吸引人的简单性和潜在效率，但迄今为止从业者对其关注有限。虽然路径采样方法广泛应用于许多类型的罕见过渡事件，但本文仅回顾了近期涉及生物分子的应用，包括异构化、蛋白质折叠和酶催化。
