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Nucleic Acids Research Advance Access originally published online on May 7, 2007
Nucleic Acids Research 2007 35(Web Server issue):W438-W443; doi:10.1093/nar/gkm288
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W438-W443
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies

Chi-Hua Tung1 and Jinn-Moon Yang1,2,3,*

1Institute of Bioinformatics, 2Department of Biological Science and Technology and 3Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, 30050 Taiwan

*To whom correspondence should be addressed. Tel: +886 3 571212 56942; Fax: +886 3 5729288; Email: moon{at}faculty.nctu.edu.tw

Received January 31, 2007. Revised April 6, 2007. Accepted April 12, 2007.

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 ~98% for 586 query structures and the average execution time is ~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.


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