Liwo Adam, Czaplewski Cezary, Ołdziej Stanisław, Scheraga Harold A
Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, United States.
Curr Opin Struct Biol. 2008 Apr;18(2):134-9. doi: 10.1016/j.sbi.2007.12.001. Epub 2008 Jan 22.
In this review, we summarize the computational methods for sampling the conformational space of biomacromolecules. We discuss the methods applicable to find only lowest energy conformations (global minimization of the potential-energy function) and to generate canonical ensembles (canonical Monte Carlo method and canonical molecular dynamics method and their extensions). Special attention is devoted to the use of coarse-grained models that enable simulations to be enhanced by several orders of magnitude.
在本综述中，我们总结了用于对生物大分子构象空间进行采样的计算方法。我们讨论了仅适用于寻找最低能量构象（势能函数的全局最小化）以及生成正则系综（正则蒙特卡罗方法和正则分子动力学方法及其扩展）的方法。我们特别关注粗粒度模型的使用，该模型能够将模拟提升几个数量级。
