FFAS (Fold & Function Assignment System) was the first structure prediction server based on profile-profile comparison. This sensitive server has the advantage of being interactive and fast. Also, it allows scanning other databases like PFAM, PDB, SCOP and COG. In addition to database searches, pairwise alignment is possible.
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Bioinformatics. 2014 Mar 1;30(5):660-7. doi: 10.1093/bioinformatics/btt578. Epub 2013 Oct 15.
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.
Xu D1, Jaroszewski L, Li Z, Godzik A.
Jaroszewski, L., Rychlewski, L., Li, Z., Li, W. & Godzik, A. (2005)
FFAS03: a server for profile-profile sequence alignments.
Nucl. Acids Res. 33, W284-W288