Sequential structure alignment program

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The sequential structure alignment program (SSAP) method uses double dynamic programming to produce a structural alignment based on atom-to-atom vectors in structure space.[1][2] Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the beta carbons 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.[3] It has been applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as CATH (Class, Architecture, Topology, Homology),.[4] which has been used to construct the 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.[5]

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  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. PMID 2769748. 
  2. ^ Orengo, C. A.; Taylor, W. R. (1996). "SSAP: Sequential structure alignment program for protein structure comparison". Methods in enzymology 266: 617–635. doi:10.1016/s0076-6879(96)66038-8. PMID 8743709. 
  3. ^ 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. PMC 2142613. PMID 7849601. 
  4. ^ 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. PMID 9309224. 
  5. ^ 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. PMID 17450548. 

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