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 ten 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 ten
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 novel structural alphabet substitution matrix.
The classification accuracy of this server is ~98% for 586 query structures and the
average execution time is ~5 seconds. This server was also evaluated using 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 hours. These results suggest
that the fastSCOP is robust and can be a useful server for recognizing the evolutionary
classification and the protein function of novel structures.
The following figure shows an overview of the fastSCOP server for rapidly recognizing SCOP domains
and evolutionary superfamilies. This sever uses 3D-BLAST to scan quickly the SCOP 1.71
database and selected the top ten hit domain structures, which are associated with different
SCOP superfamily entries (Figure 1B). MAMMOTH was then adopted to align sequentially the
query structure with each structure of the top ten structures, to refine the domain boundaries
and to recognize evolutionary superfamilies (Figures 1B and 1C).