Rapid sampling of all-atom peptides using a library-based polymer-growth approach.
Rapid sampling of all-atom peptides using a library-based polymer-growth approach.
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使用基于库的聚合物生长方法对全原子肽进行快速采样。
DOI：
10.1002/jcc.21626
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发表时间：
2011
影响因子：
3
通讯作者：
Zuckerman,DanielM
中科院分区：
文献类型：
--
作者：
Mamonov,ArtemB;Zhang,Xin;Zuckerman,DanielM
我们适应现有的聚合物生长策略的平衡采样的肽所描述的现代原子力场与一个简单的均匀的介电溶剂。我们的方法的主要新特点是使用预先计算的分子片段的统计库。通过结合储存在文库中的片段构型（在本研究中为单个残基）对分子进行取样。从独立库生成的系综被重新加权，以符合描述完整分子的力场的玻尔兹曼因子分布。通过这种方式，小肽（4-8个残基）的高质量平衡采样通常需要不到一小时的单处理器时钟时间，并且可以比Langevin模拟快得多。此外，在不到一分钟的单处理器计算中，可以为较大的肽（在本研究中多达32个残基）生成近似的无冲突集合。我们讨论了我们的生长过程的自由能计算，片段组装蛋白质结构预测协议，和“多分辨率”采样的可能应用。© 2010 Wiley Periodicals，Inc. J Comput Chem，2011年
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with a simple uniform dielectric solvent. The main novel feature of our approach is the use of precalculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations—of single residues in this study—which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann‐factor distribution of the forcefield describing the full molecule. In this way, high‐quality equilibrium sampling of small peptides (4–8 residues) typically requires less than one hour of single‐processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate, clash‐free ensembles can be generated for larger peptides (up to 32 residues in this study) in less than a minute of single‐processor computing. We discuss possible applications of our growth procedure to free energy calculation, fragment assembly protein‐structure prediction protocols, and to “multi‐resolution” sampling. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011