Mirjalili Vahid, Feig Michael
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824; USA ; Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48824; USA.
J Chem Theory Comput. 2013 Feb 12;9(2):1294-1303. doi: 10.1021/ct300962x. Epub 2012 Dec 22.
A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.
本文描述了一种基于分子动力学（MD）模拟的协议，用于基于模板的模型预测的结构优化。该协议包括应用约束、对选定子集进行系综平均、在初始结构和优化结构之间进行插值以及评估优化的成功与否。结果发现，基于亚微秒MD的采样与系综平均相结合时，对于此处考虑的CASP目标中的大多数系统，可以产生适度但一致的优化效果。
