研究环肽构象行为的计算方法
Computational Methods for Studying Conformational Behaviors of Cyclic Peptides.
作者信息
Jiang Fan, Geng Hao
机构信息
Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
出版信息
Methods Mol Biol. 2019;2001:61-71. doi: 10.1007/978-1-4939-9504-2_4.
Molecular dynamics (MD) simulations play more and more important roles in studying conformations of cyclic peptides in solution. Here we describe how to use replica-exchange molecular dynamics (REMD) implemented in Gromacs software package to simulate peptides with backbone cyclization and stapled peptides with side-chain linkages. Some of our methods for trajectory analyses and our residue-specific force fields are also described.
分子动力学（MD）模拟在研究溶液中环肽的构象方面发挥着越来越重要的作用。在此，我们描述了如何使用Gromacs软件包中实现的副本交换分子动力学（REMD）来模拟具有主链环化的肽和具有侧链连接的订书肽。我们还描述了一些轨迹分析方法和残基特异性力场。
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