Accelerated molecular dynamics in computational drug design.
Accelerated molecular dynamics in computational drug design.
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DOI：
10.1007/978-1-61779-465-0_30
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发表时间：
2012
影响因子：
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通讯作者：
Jeff Wereszczynski;J. McCammon
中科院分区：
文献类型：
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作者：
Jeff Wereszczynski;J. McCammon
加速分子动力学 (aMD) 方法已被证明可以提高生物分子模拟中相空间采样的速率。在本章中，我们讨论 aMD 背后的理论并描述两个版本的实现：双升压和选择性 aMD。每种方法都有其实际优势：双增强 aMD 对于增加全局构象运动的采样很有用，而选择性 aMD 可以提高自由能计算的收敛速度。特别强调这些方法在计算机辅助药物设计中的使用，并且在这两种情况下都强调了奥司他韦与神经氨酸酶结合的例子。
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.