imported>Citation bot: Altered title. Added chapter. | Use this bot. Report bugs. | Suggested by Headbomb | Linked from Wikipedia:WikiProject_Academic_Journals/Journals_cited_by_Wikipedia/Sandbox | #UCB_webform_linked 292/335

2024-06-22T04:10:32Z

Altered title. Added chapter. | Use this bot. Report bugs. | Suggested by Headbomb | Linked from Wikipedia:WikiProject_Academic_Journals/Journals_cited_by_Wikipedia/Sandbox | #UCB_webform_linked 292/335

New page

{{Technical|date=October 2021}}
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.
| title = Protein structure alignment
| journal = Journal of Molecular Biology
| volume = 208
| issue = 1
| pages = 1–22
| year = 1989
| pmid = 2769748
| doi=10.1016/0022-2836(89)90084-3
}}</ref><ref>{{Cite book
| last1 = Orengo | first1 = C. A.
| last2 = Taylor | first2 = W. R.
| chapter = SSAP: Sequential structure alignment program for protein structure comparison
| title = Computer Methods for Macromolecular Sequence Analysis
| series = Methods in Enzymology
| volume = 266
| pages = 617–635
| year = 1996
| 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
| last1 = Taylor | first1 = W. R.
| last2 = Flores | first2 = T. P.
| last3 = Orengo | first3 = C. A.
| doi = 10.1002/pro.5560031025
| title = Multiple protein structure alignment
| journal = Protein Science
| volume = 3
| issue = 10
| pages = 1858–1870
| year = 1994
| 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
| last1 = Porwal | first1 = G.
| last2 = Jain | first2 = S.
| last3 = Babu | first3 = S. D.
| last4 = Singh | first4 = D.
| last5 = Nanavati | first5 = H.
| last6 = Noronha | first6 = S.
| doi = 10.1002/jcc.20736
| title = Protein structure prediction aided by geometrical and probabilistic constraints
| journal = Journal of Computational Chemistry
| volume = 28
| issue = 12
| pages = 1943–1952
| year = 2007
| pmid = 17450548
| pmc =
| s2cid = 5710322
}}</ref>

==See also==
*[[Structural alignment]]
*[[CATH|Class, Architecture, Topology, Homology (CATH)]]
*[[Root mean square deviation (bioinformatics)|RMSD]] — A different structure comparison measure
*[[Template modeling score|TM-score]] — A different structure comparison measure
*[[Global distance test|GDT]] — A different structure comparison measure
*[[Longest Continuous Segment (bioinformatics)|LCS]] — A different structure comparison measure

==References==
{{reflist}}

==External links==
* [http://www.cathdb.info/cgi-bin/SsapServer.pl SSAP Server] for pairwise structural comparison

[[Category:Bioinformatics]]
[[Category:Computational chemistry]]

Sequential structure alignment program - Revision history

imported>Citation bot: Altered title. Added chapter. | Use this bot. Report bugs. | Suggested by Headbomb | Linked from Wikipedia:WikiProject_Academic_Journals/Journals_cited_by_Wikipedia/Sandbox | #UCB_webform_linked 292/335