A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features
文献类型：期刊论文
| 作者 | Liu X(刘鑫) ; Zhao YP(赵亚溥); Liu X(刘鑫); Zhao YP(赵亚溥); Zhao YP(赵亚溥)
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| 刊名 | Journal of Theoretical Biology
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| 出版日期 | 2009 |
| 卷号 | 261期号:4页码:593-597 |
| 通讯作者邮箱 | yzhao@imech.ac.cn |
| 关键词 | Scoring scheme Hydrophobic interaction Multiple sequence alignment Homologous proteins |
| ISSN号 | 0022-5193 |
| 通讯作者 | 赵亚溥 |
| 合作状况 | 其它 |
| 中文摘要 | As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably. |
| 学科主题 | 固体力学 |
| 关键词[WOS] | ACID SUBSTITUTION MATRICES; PROTEIN; COMPLEXITY; REDUCTION; ALPHABET; DATABASE; MODELS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000274799100009 |
| 公开日期 | 2009-12-28 |
| 源URL | [http://dspace.imech.ac.cn/handle/311007/28813]  |
| 专题 | 力学研究所_非线性力学国家重点实验室 |
| 通讯作者 | Zhao YP(赵亚溥) |
| 推荐引用方式 GB/T 7714 | Liu X,Zhao YP,Liu X,et al. A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features[J]. Journal of Theoretical Biology,2009,261(4):593-597. |
| APA | Liu X,Zhao YP,Liu X,Zhao YP,&赵亚溥.(2009).A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features.Journal of Theoretical Biology,261(4),593-597. |
| MLA | Liu X,et al."A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features".Journal of Theoretical Biology 261.4(2009):593-597. |
入库方式： OAI收割
来源：力学研究所
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