A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone
A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone
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DOI：
10.1002/prot.25652
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发表时间：
2019-04-01
影响因子：
2.9
通讯作者：
Montalvao, Rinaldo Wander
中科院分区：
文献类型：
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作者：
da Silva Neto, Antonio Marinho;Silva, Samuel Reghim;Montalvao, Rinaldo Wander
这里的微分几何（DG）表示的蛋白质骨干是探讨蛋白质构象集成分析。用曲率、kappa和扭矩、tau值来描述蛋白质骨架，提出了1)一种新的不相似性和蛋白质柔韧性测量方法和2)一种局部构象聚类方法。将该方法应用于泛素和c-Myb-KIX蛋白构象集成，结果表明kappa\tau度量空间可以通过避免叠加问题来正确判断蛋白质的灵活性。与RMSF相比，d（max）测量结果同样好或更好，特别是对于本质上非结构化的蛋白质。聚类方法的独特之处在于，它通过提供每个残基的全局聚类解决方案，将蛋白质全局与局部动力学联系起来。所提出的方法对分析高度柔性的蛋白质特别有用。为本文提供的分析编写的软件仅供学术使用。
Here a differential geometry (DG) representation of protein backbone is explored on the analyses of protein conformational ensembles. The protein backbone is described by curvature, kappa, and torsion, tau, values per residue and we propose 1) a new dissimilarity and protein flexibility measurement and 2) a local conformational clustering method. The methods were applied to Ubiquitin and c-Myb-KIX protein conformational ensembles and results show that kappa\tau metric space allows to properly judge protein flexibility by avoiding the superposition problem. The d(max) measurement presents equally good or superior results when compared to RMSF, especially for the intrinsically unstructured protein. The clustering method is unique as it relates protein global to local dynamics by providing a global clustering solutions per residue. The methods proposed can be especially useful to the analyses of highly flexible proteins. The software written for the analyses presented here is available at for academic usage only.