Bastolla U, Frauenkron H, Gerstner E, Grassberger P, Nadler W
HLRZ, c/o Forschungszentrum Jülich, Germany.
Proteins. 1998 Jul 1;32(1):52-66.
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (PERM) (Grassberger, Phys. Rev. E 56:3682, 1997) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare it to published Monte Carlo studies of the properties of particular sequences. In all cases our method is faster than the previous ones, and in several cases we find new minimal energy states. In addition to producing more reliable candidates for ground states, our method gives detailed information about the thermal spectrum and thus allows one to analyze thermodynamic aspects of the folding behavior of arbitrary sequences.
我们证明,最近提出的剪枝富集罗森布鲁斯方法(PERM)(格拉斯伯格,《物理评论E》56:3682,1997)能产生用于简单模型蛋白质折叠的极其高效的算法。我们在几种晶格杂聚物模型上对其进行测试,并将其与已发表的关于特定序列性质的蒙特卡罗研究进行比较。在所有情况下,我们的方法都比以前的方法更快,并且在几种情况下我们发现了新的最低能量状态。除了为基态产生更可靠的候选者外,我们的方法还给出了有关热谱的详细信息,从而使人们能够分析任意序列折叠行为的热力学方面。