Comparisons of force fields for proteins by generalized-ensemble simulations
Comparisons of force fields for proteins by generalized-ensemble simulations
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DOI：
10.1016/j.cplett.2004.01.078
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发表时间：
2004-03-11
影响因子：
2.8
通讯作者：
Okamoto, Y
中科院分区：
文献类型：
--
作者：
Yoda, T;Sugita, Y;Okamoto, Y
比较了不同研究小组提出的六种常用蛋白质力场的二级结构特征。我们进行了分子动力学模拟的α-螺旋多肽和β-发夹多肽与明确的水分子。两个广义集成算法，复制交换多规范算法和多规范复制交换方法，有效的采样配置空间已被采用。比较不同力场作用下多肽二级结构的含量，可以看出其结构倾向的差异。结果表明，AMBER 94和AMBER 99更倾向于α-螺旋，而GROMOS 96更倾向于β-发夹，而CHARNIM 22、AMBER 96和OPLS-AA/L具有中间趋势。(C)2004年由Elsevier B. V.出版
Secondary structural characteristics of six commonly used force fields for protein systems developed by different research groups have been compared. We performed molecular dynamics simulations of an alpha-helical polypeptide and a beta-hairpin polypeptide with explicit water molecules. Two generalized-ensemble algorithms, replica-exchange multicanonical algorithm and multicanonical replica-exchange method, for efficient sampling of configurational space have been employed. Comparisons of the secondary structure content of polypeptides for different force fields highlighted differences of their structural tendency. The results imply that a-helix is favored for AMBER94 and AMBER99 and that beta-hairpin is favored for GROMOS96, while CHARNIM22, AMBER96, and OPLS-AA/L have intermediate tendency. (C) 2004 Published by Elsevier B.V.