Protein Structure Alignment Based on Internal Coordinates
文献类型：期刊论文
| 作者 | Shen, Yue-Feng1,2; Li, Bo1,2 ; Liu, Zhi-Ping1
|
| 刊名 | INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000208709300002 |
| 出版者 | SPRINGER HEIDELBERG |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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