Methods for Monte Carlo simulations of biomacromolecules.
Methods for Monte Carlo simulations of biomacromolecules.
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DOI：
10.1016/s1574-1400(09)00503-9
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发表时间：
2009-01-01
期刊：
影响因子：
--
通讯作者：
Pappu RV
中科院分区：
文献类型：
--
作者：
Vitalis A;Pappu RV
综述了生物大分子蒙特卡罗模拟的研究现状。鉴于溶剂环境的连续描述，对经典系综中生物大分子的构象平衡和缔合的采样方法进行了综述。提供了详细的章节处理自由度的选择，MC算法的效率和算法的特点，以及简单的移动集的优化。将相关性引入基本MC移动的问题，以及这种方法对生物大分子模拟的适用性进行了讨论。还提供了一个简短的讨论，多规范的方法和最近的模拟工作的概述突出MC方法的潜力。有人认为，MC模拟，而未充分利用的生物大分子模拟社区，持有承诺的复杂系统和现象，跨越多个长度尺度的模拟，特别是当使用隐式溶剂化模型或其他粗粒化策略结合。
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves, and the applicability of such methods to simulations of biomacromolecules is discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, while underutilized biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse graining strategies.