fastSCOP -- a fast web server for recognizing protein structural domains and SCOP superfamilies
What you can do:
Input a protein structure as a query to assign the SCOP domains and evolutionary classifications.
Highlights:
- 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 approximately 98% for 586 query structures and the average execution time is approximately 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.
Keywords:
- Amino Acid Sequence
- Molecular Sequence Data
- Protein Conformation
- Protein Structure
- Sequence Analysis
- Sequence Homology
- Structural Homology
- SCOP
- evolutionary classification
- structural domains
- evolutionary superfamilies
Literature & Tutorials:
This record last updated: 06-03-2008