Sequential structure alignment program

The SSAP (Sequential Structure Alignment Program) 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]

See also

• Structural alignment
• Class, Architecture, Topology, Homology (CATH)
• RMSD — A different structure comparison measure
• TM-Score — A different structure comparison measure
• GDT — A different structure comparison measure
• LCS — A different structure comparison measure

References

1. Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 2769748, please use {{cite journal}} with |pmid=2769748 instead.
2. Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 8743709, please use {{cite journal}} with |pmid=8743709 instead.
3. Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 7849601, please use {{cite journal}} with |pmid=7849601 instead.
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. Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17450548, please use {{cite journal}} with |pmid=17450548 instead.

External links

• SSAP Server for pairwise structural comparison