Analysis of protein dynamics using local-DME calculations.
Analysis of protein dynamics using local-DME calculations.
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DOI：
10.1504/ijbra.2011.040093
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发表时间：
2011
影响因子：
--
通讯作者：
Zhijun Wu
中科院分区：
文献类型：
--
作者：
Wu D;Smith S;Mahan H;Jernigan RL;Zhijun Wu
蛋白质结构的灵活性和动态性反映在B因子和顺序参数中，这些参数是通过X射线晶体学和核磁共振（NMR）实验获得的。诸如简正模分析（NMA）和弹性网络模型（ENM）的方法可以用于预测蛋白质结构的原子水平或粗粒度结构的波动。在这里，我们介绍了本地距离矩阵误差（DME），一个有效的和简单的分析方法来研究蛋白质结构的波动，特别是对于NMR确定的蛋白质结构的集合。与实验和其他计算得到的波动比较显示出很强的相关性。
Flexibility and dynamics of protein structures are reflected in the B-factors and order parameters obtained experimentally with X-ray crystallography and Nuclear Magnetic Resonance (NMR). Methods such as Normal Mode Analysis (NMA) and Elastic Network Models (ENM) can be used to predict the fluctuations of protein structures for either atomic level or coarse-grained structures. Here, we introduce the Local-Distance Matrix Error (DME), an efficient and simple analytic method to study the fluctuations of protein structures, especially for the ensembles of NMR-determined protein structures. Comparisons with the fluctuations obtained by experiments and other by computations show strong correlations.