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The '''SSAP''' ('''Sequential Structure Alignment Program''') method uses double [[dynamic programming]] to produce a structural alignment based on atom-to-atom [[Vector (geometric)|vectors]] in structure space. Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the [[beta carbon]]s for all residues except glycine, a method which thus takes into account the rotameric state of each residue as well as its ___location along the backbone. SSAP works by first constructing a series of inter-residue distance vectors between each residue and its nearest non-contiguous neighbors on each protein. A series of matrices are then constructed containing the vector differences between neighbors for each pair of residues for which vectors were constructed. Dynamic programming applied to each resulting matrix determines a series of optimal local alignments which are then summed into a "summary" matrix to which dynamic programming is applied again to determine the overall structural alignment.
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.
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