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Protein Structure Alignment Based on Internal Coordinates
Shen, Yue-Feng1,2; Li, Bo1,2; Liu, Zhi-Ping1
2010-12-01
发表期刊INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
ISSN1913-2751
卷号2期号:4页码:308-319
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).
关键词protein structure alignment internal coordinate difference matrix structural bioinformatics
DOI10.1007/s12539-010-0019-8
语种英语
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
WOS类目Mathematical & Computational Biology
WOS记录号WOS:000208709300002
出版者SPRINGER HEIDELBERG
引用统计
文献类型期刊论文
条目标识符http://ir.amss.ac.cn/handle/2S8OKBNM/9702
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
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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.
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