Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Curr Opin Pharmacol. 2010 Dec;10(6):745-52. doi: 10.1016/j.coph.2010.09.008. Epub 2010 Oct 8.
Molecular dynamics (MD) simulations can provide atomically detailed views of protein motions, sampling multiple timescales ranging from femtoseconds to nanoseconds on typical computing resources. The 'reach' of these computer simulations toward biologically relevant timescales (microseconds and beyond) has been improving with advances in hardware and software, as well as the development of enhanced sampling techniques. This review outlines these advances, focusing on techniques that also provide realistic, unperturbed kinetics. These longer-timescale MD simulations can provide detailed insights into the mechanisms of biological events, potentially aiding the design of pharmaceuticals.
分子动力学（MD）模拟可以提供蛋白质运动的原子级详细视图，在典型的计算资源上，从飞秒到纳秒的多个时间尺度进行采样。随着硬件和软件的进步以及增强采样技术的发展，这些计算机模拟在生物相关时间尺度（微秒及以上）上的“可达性”得到了提高。本文综述了这些进展，重点介绍了那些还提供真实、未受干扰的动力学的技术。这些更长时间尺度的 MD 模拟可以提供对生物事件机制的详细见解，有可能辅助药物设计。
