The sequential structure alignment program (SSAP)inchemistry, physics, and biology is a method that 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]
^Orengo, C. A.; Taylor, W. R. (1996). "SSAP: Sequential structure alignment program for protein structure comparison". Computer Methods for Macromolecular Sequence Analysis. Methods in Enzymology. Vol. 266. pp. 617–635. doi:10.1016/s0076-6879(96)66038-8. ISBN9780121821678. PMID8743709.
