Protein structure alignment using elastic shape analysis
Protein structure alignment using elastic shape analysis
复制标题
使用弹性形状分析进行蛋白质结构比对
DOI：
--
复制
发表时间：
2010
期刊：
影响因子：
--
通讯作者：
Jinfeng Zhang
中科院分区：
文献类型：
--
作者：
W. Liu;Anuj Srivastava;Jinfeng Zhang
在本文中，我们提出了一种方法，灵活的蛋白质结构对齐的基础上弹性形状分析的骨干，在某种程度上，可以将不同的特点的骨干。特别地，它可以包括匹配过程中的骨架几何结构、二级结构和氨基酸序列。因此，可以计算形式距离，并且可以计算任何两个骨架结构的测地线路径，其显示构象/结构之间的最佳变形。它也可以用来平均形状的构象与类似的蛋白质。使用SCOP和PDB数据库中的蛋白质，我们展示了使用骨架几何形状，二级标签和一级序列的蛋白质的匹配和聚类。我们证明了近92%的成功率在自动聚类的100个蛋白质从SCOP数据库。
In this paper we present a method for flexible protein structure alignment based on elastic shape analysis of backbones, in a manner that can incorporate different characteristics of the backbones. In particular, it can include the backbone geometry, the secondary structures, and the amino-acid sequences in the matching process. As a result, a formal distance can be calculated and geodesic paths, showing optimal deformations between conformations/structures, can be computed for any two backbone structures. It can also be used to average shapes of conformations associated with similar proteins. Using proteins from SCOP and PDB databases we demonstrate the matching and clustering of proteins using the backbone geometries, the secondary labels and the primary sequences. We demonstrate almost 92% success rate in automatic clustering of 100 proteins from SCOP database.