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 o

SUBMITTER: Tung CH 

PROVIDER: S-EPMC1933144 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature