Using dihedral angle series of protein for protein structure comparison

doi:10.3778/j.issn.1002-8331.2009.32.002

Computer Engineering and Applications ›› 2009, Vol. 45 ›› Issue (32): 5-8.DOI: 10.3778/j.issn.1002-8331.2009.32.002

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Using dihedral angle series of protein for protein structure comparison

GAO Jian-zhao，HU Gang，WANG Kui，CUI Jia-feng

School of Mathematical Sciences and LPMC，Nankai University，Tianjin 300071，China

Received:2009-08-05 Revised:2009-09-15 Online:2009-11-11 Published:2009-11-11
Contact: GAO Jian-zhao

利用蛋白质的二面角序列对蛋白质结构比对

高建召，胡刚，王奎，崔家峰

南开大学数学科学学院与LPMC，天津 300071

通讯作者: 高建召

Abstract

Abstract: Protein structure comparison is very important to protein function and evolution.This paper proposes a novel algorithm based on dihedral angle.It uses dynamic time warping to align angle series.After fitting the distribution of aligned score，it uses p-value to evaluate the result of alignment.The results reported here show that （1）The aligned score is a good similarity measure in analysis of the protein.（2）Aligned score is following the generalized extreme value distribution with parameters μ=94.769 7，σ=41.583 7，ξ=0.192 5.（3）Compared with other algorithm of structure alignment，the algorithm performs better than CTSS.

Key words: protein structure comparison, generalized extreme value distribution, dihedral angle series, dynamic time warping, p-value

摘要： 蛋白质结构比对对理解蛋白质功能和进化关系非常重要。提出一种基于蛋白质残基的二面角的结构比对算法。通过动态时间规整算法比对二面角序列，来比较蛋白质的结构，拟合两蛋白结构距离的分布后，利用p-value来评价比对的好坏。主要结果有：利用动态时间规整算法计算得出的结构距离是一个很好的蛋白质结构相似性度量；结构距离服从参数为μ=94.769 7，σ=41.583 7，ξ=0.192 5的广义的极值分布；和其他结构比对算法相比，该算法比CTSS的搜索结果要好。

关键词: 蛋白质结构比对, 广义极值分布, 二面角序列, 动态时间规整, p-value

CLC Number:

O236

GAO Jian-zhao，HU Gang，WANG Kui，CUI Jia-feng. Using dihedral angle series of protein for protein structure comparison[J]. Computer Engineering and Applications, 2009, 45(32): 5-8.

高建召，胡刚，王奎，崔家峰. 利用蛋白质的二面角序列对蛋白质结构比对[J]. 计算机工程与应用, 2009, 45(32): 5-8.

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Using dihedral angle series of protein for protein structure comparison

利用蛋白质的二面角序列对蛋白质结构比对

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