CABS-flex predictions of protein flexibility compared with NMR ensembles
CABS-flex predictions of protein flexibility compared with NMR ensembles
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DOI：
10.1093/bioinformatics/btu184
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发表时间：
2014-08-01
期刊：
影响因子：
5.8
通讯作者：
Kmiecik, Sebastian
中科院分区：
文献类型：
--
作者：
Jamroz, Michal;Kolinski, Andrzej;Kmiecik, Sebastian
动机：识别蛋白质结构的柔性区域对于理解其生物学功能非常重要。最近，我们已经开发出一种快速的方法来预测蛋白质结构波动从一个单一的蛋白质模型：CABS-flex。CABS-flex被证明是传统全原子分子动力学（MD）的有效替代方案。在这项工作中，我们评估CABS-Flex和MD预测的NMR ensembles.Results内的蛋白质结构变化的比较：基于一个基准集的140种蛋白质，我们表明，从CABS-Flex获得的蛋白质残基的相对波动是很好的相关性NMR ensembles。平均而言，这种相关性比MD和NMR系综之间的相关性更强。总之，CABS-flex是有用的和互补的MD在预测蛋白质区域经历构象变化以及这种变化的程度。
Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics ( MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes.