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Protein Structure Alignment Based on Internal Coordinates
Shen, Yue-Feng1,2; Li, Bo1,2; Liu, Zhi-Ping1
AbstractProtein 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).
Keywordprotein structure alignment internal coordinate difference matrix structural bioinformatics
Funding ProjectNational Natural Science Foundation of China (NSFC)[10801131] ; National Natural Science Foundation of China (NSFC)[10771206] ; 973 Project[2004CB318000]
WOS Research AreaMathematical & Computational Biology
WOS SubjectMathematical & Computational Biology
WOS IDWOS:000208709300002
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Document Type期刊论文
Corresponding AuthorLiu, Zhi-Ping
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
Recommended Citation
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.
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