KMS Of Academy of mathematics and systems sciences, CAS
| Protein Structure Alignment Based on Internal Coordinates | |
Shen, Yue-Feng1,2; Li, Bo1,2 ; Liu, Zhi-Ping1
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| 2010-12-01 | |
| Source Publication | INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
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| ISSN | 1913-2751 |
| Volume | 2Issue:4Pages:308-319 |
| Abstract | 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). |
| Keyword | protein structure alignment internal coordinate difference matrix structural bioinformatics |
| DOI | 10.1007/s12539-010-0019-8 |
| Language | 英语 |
| Funding Project | National Natural Science Foundation of China (NSFC)[10801131] ; National Natural Science Foundation of China (NSFC)[10771206] ; 973 Project[2004CB318000] |
| WOS Research Area | Mathematical & Computational Biology |
| WOS Subject | Mathematical & Computational Biology |
| WOS ID | WOS:000208709300002 |
| Publisher | SPRINGER HEIDELBERG |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/9702 |
| Collection | 系统科学研究所 |
| Corresponding Author | Liu, Zhi-Ping |
| Affiliation | 1.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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