Wereszczynski Jeff, McCammon J Andrew
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA.
Methods Mol Biol. 2012;819:515-24. doi: 10.1007/978-1-61779-465-0_30.
The method of accelerated molecular dynamics (aMD) has been shown to increase the rate of phase-space sampling in biomolecular simulations. In this chapter, we discuss the theory behind aMD and describe the implementation of two versions: dual-boost and selective aMD. Each method has its practical advantages: dual-boost aMD is useful for increasing sampling of global conformational motions while selective aMD can improve the rate of convergence of free energy calculations. Special emphasis is placed on the use of these methods in computer-aided drug design, and the example of oseltamivir binding to neuraminidase is highlighted for both cases.
加速分子动力学（aMD）方法已被证明可提高生物分子模拟中的相空间采样速率。在本章中，我们将讨论aMD背后的理论，并描述两个版本的实现：双增强和选择性aMD。每种方法都有其实际优势：双增强aMD有助于增加全局构象运动的采样，而选择性aMD可以提高自由能计算的收敛速率。我们特别强调这些方法在计算机辅助药物设计中的应用，并以两种情况下的奥司他韦与神经氨酸酶结合为例进行说明。
