基于物理的蛋白质结构优化：通过多条分子动力学轨迹和结构平均化实现
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.
作者信息
Mirjalili Vahid, Noyes Keenan, Feig Michael
机构信息
Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, 48824; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824.
出版信息
Proteins. 2014 Feb;82 Suppl 2(0 2):196-207. doi: 10.1002/prot.24336. Epub 2013 Aug 19.
Abstract
We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.
摘要
我们使用分子动力学（MD）模拟对蛋白质结构预测技术关键评估10（CASP10）目标进行结构优化。通过从基于MD的系综中选择结构，然后进行结构平均来实现优化。描述了该方法在CASP10中的整体性能，并详细分析了具体方面，以深入了解关键组成部分。特别是，详细讨论了不同约束类型的使用、从多个短模拟与单个长模拟中采样、质量评估标准的成功性、评分与平均的应用以及最终优化步骤的影响。
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