The use of a conformational alphabet for fast alignment of protein structures
文献类型：会议论文
| 作者 | Zheng, WM
|
| 出版日期 | 2008 |
| 会议日期 | MAY 06-09, 2008 |
| 会议地点 | Georgia State Univ, Atlanta, GA |
| 关键词 | SUBSTITUTION MATRIX ALGORITHM CE |
| 卷号 | 4983 |
| 页码 | 331-342 |
| 英文摘要 | A protein conformational alphabet refers to the discretized states of the three-dimensional segmental structure of protein backbones. Here a letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues, and our alphabet consist of 17 letters obtained by clustering based on the probability distribution of these angles. A substitution matrix called CLESUM has been derived from an alignment database of representative structures to measure both evolutionary and geometrical similarity between any two such letters. A structural fragment is then mapped to a string, and two strings with their CLESUM score being higher than a preset threshold form a similar fragment pair (SFP). The search for SFPs by string comparison is fast. Furthermore, CLESUM scores reflect the importance of SFPs to structure alignment, and then the search space can be significantly-reduced. A fast tool for pairwise alignment called CLePAPS is developed by collecting as many spatially consistent SFPs a's possible. Extending the concept of SFPs to that of similar fragment blocks for multiple structure alignment leads to a fast tool for multiple structure alignment called BLOMAPS. Both CLePAPS and BLOMAPS are tested on ensembles of various structures. They are reliable, and about two or three orders faster than some well-known algorithms. |
| 源文献作者 | Georgia State Univ |
| 会议录 | BIOINFORMATICS RESEARCH AND APPLICATIONS
 |
| 会议录出版者 | SPRINGER-VERLAG BERLIN |
| 会议录出版地 | BERLIN |
| 语种 | 英语 |
| ISSN号 | 0302-9743 |
| WOS研究方向 | Biochemistry & Molecular Biology ; Computer Science ; Mathematical & Computational Biology |
| ISBN号 | 978-3-540-79449-3 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/23661]  |
| 专题 | SCI会议论文 |
| 作者单位 | Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zheng, WM. The use of a conformational alphabet for fast alignment of protein structures[C]. 见:. Georgia State Univ, Atlanta, GA. MAY 06-09, 2008. |
入库方式： OAI收割
来源：理论物理研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。