# Sequential structure alignment program

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The **sequential structure alignment program (SSAP)** in [chemistry](/source/Chemistry), [physics](/source/Physics), and [biology](/source/Biology) is a method that uses double [dynamic programming](/source/Dynamic_programming) to produce a structural alignment based on atom-to-atom [vectors](/source/Vector_(geometric)) in structure space.[1][2] Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the [beta carbons](/source/Beta_carbon) for all residues except glycine, a method which thus takes into account the [rotameric state](https://en.wiktionary.org/wiki/rotamer) 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.[3] It has been applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as [CATH](/source/CATH) (Class, Architecture, Topology, Homology),.[4] which has been used to construct the [CATH Protein Structure Classification](https://web.archive.org/web/20070517161248/http://www.cathdb.info/latest/index.html) 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.[5]

## See also

- [Structural alignment](/source/Structural_alignment)
- [Class, Architecture, Topology, Homology (CATH)](/source/CATH)
- [RMSD](/source/Root_mean_square_deviation_(bioinformatics)) — A different structure comparison measure
- [TM-score](/source/Template_modeling_score) — A different structure comparison measure
- [GDT](/source/Global_distance_test) — A different structure comparison measure
- [LCS](/source/Longest_Continuous_Segment_(bioinformatics)) — A different structure comparison measure

## References

1. Taylor, W. R. & Orengo, C. A. (1989). "Protein structure alignment". *Journal of Molecular Biology*. **208** (1): 1–22. [doi:10.1016/0022-2836(89)90084-3](https://doi.org/10.1016/0022-2836(89)90084-3). [PMID 2769748](https://pubmed.ncbi.nlm.nih.gov/2769748)

1. Orengo, C. A. & Taylor, W. R. (1996). "SSAP: Sequential structure alignment program for protein structure comparison". *Computer Methods for Macromolecular Sequence Analysis*. Vol. 266. Methods in Enzymology. pp. 617–635. [doi:10.1016/s0076-6879(96)66038-8](https://doi.org/10.1016/s0076-6879(96)66038-8). ISBN 9780121821678. [PMID 8743709](https://pubmed.ncbi.nlm.nih.gov/8743709)

1. Taylor, W. R.; Flores, T. P.; Orengo, C. A. (1994). "Multiple protein structure alignment". *Protein Science*. **3** (10): 1858–1870. [doi:10.1002/pro.5560031025](https://doi.org/10.1002/pro.5560031025). [PMC 2142613](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142613). [PMID 7849601](https://pubmed.ncbi.nlm.nih.gov/7849601)

1. Orengo CA; Michie AD; Jones S; Jones DT; Swindells MB; Thornton JM (1997). "CATH—a hierarchic classification of protein domain structures". *Structure*. **5** (8): 1093–1108. [doi:10.1016/S0969-2126(97)00260-8](https://doi.org/10.1016/S0969-2126(97)00260-8). [PMID 9309224](https://pubmed.ncbi.nlm.nih.gov/9309224)

1. Porwal, G.; Jain, S.; Babu, S. D.; Singh, D.; Nanavati, H.; Noronha, S. (2007). "Protein structure prediction aided by geometrical and probabilistic constraints". *Journal of Computational Chemistry*. **28** (12): 1943–1952. [doi:10.1002/jcc.20736](https://doi.org/10.1002/jcc.20736). [PMID 17450548](https://pubmed.ncbi.nlm.nih.gov/17450548). [S2CID 5710322](https://api.semanticscholar.org/CorpusID:5710322)

## External links

- [SSAP Server](http://www.cathdb.info/cgi-bin/SsapServer.pl) for pairwise structural comparison

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