FFAS03: a server for profile-profile sequence alignments
Top Cited Papers
Open Access
- 1 July 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (Web Server) , W284-W288
- https://doi.org/10.1093/nar/gki418
Abstract
The FFAS03 server provides a web interface to the third generation of the profile-profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. As a result, they enable detection of remote homologies beyond the reach of other methods. FFAS, initially developed in 2000, is consistently one of the best ranked fold prediction methods in the CAFASP and LiveBench competitions. It is also used by several fold-recognition consensus methods and meta-servers. The FFAS03 server accepts a user supplied protein sequence and automatically generates a profile, which is then compared with several sets of sequence profiles of proteins from PDB, COG, PFAM and SCOP. The profile databases used by the server are automatically updated with the latest structural and sequence information. The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org.Keywords
This publication has 32 references indexed in Scilit:
- Structure of the apoptotic protease-activating factor 1 bound to ADPNature, 2005
- Solution Structure of a Ubiquitin-like Domain from Tubulin-binding Cofactor BPublished by Elsevier ,2004
- Protein structure prediction and analysis using the Robetta serverNucleic Acids Research, 2004
- The importance of alignment accuracy for molecular replacementActa Crystallographica Section D-Biological Crystallography, 2004
- CAFASP‐1: Critical assessment of fully automated structure prediction methodsProteins-Structure Function and Bioinformatics, 1999
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Searching databases of conserved sequence regions by aligning protein multiple-alignments [published erratum appears in Nucleic Acids Res 1996 Nov 1;24(21):4372]Nucleic Acids Research, 1996
- [33] Analysis of compositionally biased regions in sequence databasesPublished by Elsevier ,1996
- SCOP: a structural classification of proteins database for the investigation of sequences and structures.Journal of Molecular Biology, 1995
- A database of protein structure families with common folding motifsProtein Science, 1992