標題: | fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies |
作者: | Tung, Chi-Hua Yang, Jinn-Moon 生物科技學系 生物資訊及系統生物研究所 Department of Biological Science and Technology Institude of Bioinformatics and Systems Biology |
公開日期: | 1-Jul-2007 |
摘要: | The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top 10 hit domains, which have different superfamily classifications, are obtained from the hit lists. MAMMOTH, a detailed structural alignment tool, is adopted to align these top 10 structures to refine domain boundaries and to identify evolutionary superfamilies. Our previous works demonstrated that 3D-BLAST is as fast as BLAST, and has the characteristics of BLAST (e.g. a robust statistical basis, effective search and reliable database search capabilities) in large structural database searches based on a structural alphabet database and a structural alphabet substitution matrix. The classification accuracy of this server is similar to 98% for 586 query structures and the average execution time is similar to 5. This server was also evaluated on 8700 structures, which have no annotations in the SCOP; the server can automatically assign 7311 (84%) proteins (9420 domains) to the SCOP superfamilies in 9.6 h. These results suggest that the fastSCOP is robust and can be a useful server for recognizing the evolutionary classifications and the protein functions of novel structures. The server is accessible at http://fastSCOP.life.nctu.edu.tw. |
URI: | http://dx.doi.org/10.1093/nar/gkm288 http://hdl.handle.net/11536/10618 |
ISSN: | 0305-1048 |
DOI: | 10.1093/nar/gkm288 |
期刊: | NUCLEIC ACIDS RESEARCH |
Volume: | 35 |
Issue: | |
起始頁: | W438 |
結束頁: | W443 |
Appears in Collections: | Articles |
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