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SSAP originally produced only pairwise alignments but has since been extended to multiple alignments as well.<ref name="taylor">Taylor WR, Flores TP, Orengo CA. (1994). Multiple protein structure alignment. ''Protein Sci'' 3(10):1858-70.</ref> It has been applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as [[CATH]] (Class, Architecture, Topology, Homology),<ref name="orengo">Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. (1997) CATH: A hierarchical classification of protein ___domain structures. ''Structure'' 5(8): 1093-1108.</ref> which has been used to construct the [http://www.cathdb.info/latest/index.html CATH Protein Structure Classification] database.
Generally, SSAP scores above 80 are associated with highly similar structures. Scores between 70 and 80 indicate a similar fold with minor variations. Structures yielding a score between 60 and 70 do not generally contain the same fold, but usually belong to the same protein class with common structural motifs<ref name="porwal">Porwal G, Jain S, Babu SD, Singh D, Nanavati H, Noronha S. (2007) Protein Structure Prediction Aided by Geometrical and Probabilistic Constraints. ''J. Comput. Chem.'' 28(12): 1943-1952.</ref>.
==See also==
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