Paper Info
Title
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.
Abstract
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.
Year
DOI
Venue
2007
10.1093/nar/gkm288
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
protein conformation,protein structure,proteins,amino acid sequence,computational biology,internet
Structural alignment,Biology,Information retrieval,Database search engine,Software,Bioinformatics,Genetics,Substitution matrix,The Internet,Alphabet,Web server,Protein structure
Journal
Volume
Issue
ISSN
35
SUPnan
0305-1048
Citations 
PageRank 
References 
5
0.51
4
Authors
2
Name
Order
Citations
PageRank
Chi-Hua Tung150.51
Jinn-moon Yang236435.89