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 | |
2010-12-01 | |
发表期刊 | INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES |
ISSN | 1913-2751 |
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 |
DOI | 10.1007/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 |
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. |
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