Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures
Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures
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DOI：
10.1063/1.1289533
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发表时间：
2000-09-22
影响因子：
4.4
通讯作者：
Skolnick, J
中科院分区：
文献类型：
--
作者：
Gront, D;Kolinski, A;Skolnick, J
采用熵抽样Monte Carlo方法、复制方法和经典的大都会格式对简单面心立方晶格聚合物的塌缩相变进行了数值研究。该模型的力场由成对的，接触型的，长程相互作用和一个基于模型中假设的β-片层定义的短程势组成。通过各种蒙特卡罗方法和与每个相关的计算成本找到最低能量构象的能力进行了检查。结果表明，所有的方法一般提供了相同的图片的崩溃过渡。然而，最完整的热力学描述的过渡来自熵抽样蒙特卡罗模拟的结果，但这是最耗时的方法。副本的方法被证明是最有效的和高效的搜索最低能量构象。简要讨论了这些研究结果的模拟策略的折叠模型蛋白质的发展可能产生的后果。(C)2000年美国物理学会。[S0021-9606（00）50836-8]。
Entropy sampling Monte Carlo, the replica method, and the classical Metropolis scheme were applied in numerical studies of the collapse transition in a simple face-centered cubic lattice polymer. The force field of the model consists of pairwise, contact-type, long-range interactions and a short-range potential based on the beta-sheet definition assumed in the model. The ability to find the lowest energy conformation by various Monte Carlo methods and the computational cost associated with each was examined. It is shown that all of the methods generally provide the same picture of the collapse transition. However, the most complete thermodynamic description of the transition derives from the results of entropy sampling Monte Carlo simulations, but this is the most time-consuming method. The replica method is shown to be the most effective and efficient in searching for the lowest energy conformation. The possible consequences of these findings for the development of simulation strategies for the folding of model proteins are discussed briefly. (C) 2000 American Institute of Physics. [S0021-9606(00)50836-8].