Protein Structure Alignment Based on Internal Coordinates

doi:10.1007/s12539-010-0019-8

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	Protein Structure Alignment Based on Internal Coordinates
	Shen, Yue-Feng 1,2; Li, Bo1,2 ; Liu, Zhi-Ping 1
刊名	INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
	2010-12-01
卷号	2 期号:4 页码:308-319
关键词	protein structure alignment internal coordinate difference matrix structural bioinformatics
ISSN号	1913-2751
DOI	10.1007/s12539-010-0019-8
英文摘要	Protein structure alignment provides an effective way to detect and analyze fold mechanism, evolutionary history and biological function of proteins. In this work, we introduced a novel method named SABIC for protein structure alignment based on the internal coordinates (i.e. bond lengths, bond angles and torsion angles) of structure representation. SABIC provides multi-alignments as the output, from which various aspects of structural similarities between proteins can be identified. The experimental results on benchmark datasets show that SABIC performs better than other popular algorithms, such as DALI, CE and SSM. Using a new defined mQ-score of alignment, SABIC performs consistently better in detecting structural classifications of proteins. In addition, we detected the extreme value distribution form statistics of mQ-score, and then the statistical significance P-value of alignment can be obtained simultaneously. The presented SABIC algorithm has been implemented in C++ and the software is available (http://www.aporc.org/doc/wiki/SABIC).
资助项目	National Natural Science Foundation of China (NSFC)[10801131] ; National Natural Science Foundation of China (NSFC)[10771206] ; 973 Project[2004CB318000]
WOS研究方向	Mathematical & Computational Biology
语种	英语
出版者	SPRINGER HEIDELBERG
WOS记录号	WOS:000208709300002
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/9701]
专题	系统科学研究所
通讯作者	Liu, Zhi-Ping
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Shen, Yue-Feng,Li, Bo,Liu, Zhi-Ping. Protein Structure Alignment Based on Internal Coordinates[J]. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES,2010,2(4):308-319.
APA	Shen, Yue-Feng,Li, Bo,&Liu, Zhi-Ping.(2010).Protein Structure Alignment Based on Internal Coordinates.INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES,2(4),308-319.
MLA	Shen, Yue-Feng,et al."Protein Structure Alignment Based on Internal Coordinates".INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES 2.4(2010):308-319.