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The '''sequential structure alignment program (SSAP)''' in [[chemistry]], [[physics]], and [[biology]] is a method that uses double [[dynamic programming]] to produce a structural alignment based on atom-to-atom [[Vector (geometric)|vectors]] in structure space.<ref>{{Cite journal
| last1 = Taylor | first1 = W. R.
| last2 = Orengo | first2 = C. A.
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| pmid = 2769748
| doi=10.1016/0022-2836(89)90084-3
}}</ref><ref>{{Cite
| last1 = Orengo | first1 = C. A.
| last2 = Taylor | first2 = W. R.
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| series = Methods in Enzymology
| volume = 266
| pages = 617–635
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| pmid = 8743709
| doi=10.1016/s0076-6879(96)66038-8
| isbn = 9780121821678
}}</ref> 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 [[wikt:rotamer|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">{{Cite journal
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| pmid = 7849601
| pmc =2142613
}}</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="Orengo1997">{{cite journal |author1=Orengo CA |author2=Michie AD |author3=Jones S |author4=Jones DT |author5=Swindells MB |author6=Thornton JM |title=CATH—a hierarchic classification of protein ___domain structures |journal=Structure |volume=5 |issue=8 |pages=1093–1108 |year=1997 |pmid=9309224 |doi=10.1016/S0969-2126(97)00260-8|doi-access=free }}</ref> which has been used to construct the [https://web.archive.org/web/20070517161248/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">{{Cite journal
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| pmid = 17450548
| pmc =
| s2cid = 5710322
}}</ref>
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