What is fastSCOP

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).