Structural Biochemistry, Bioinformatics, Structural Alignments, Programs Used For Structural Alignment, SSAP

SSAP

Illustration of the atom-to-atom vectors calculated in SSAP. From these vectors, a series of vector differences can be constructed, for example, between (FA) in Protein 1 and (SI) in Protein 2. The two sequences are plotted on the two dimensions of a matrix to form a difference matrix between the two proteins. Dynamic programming is applied to all possible difference matrices to build a series of optimal local alignment paths that are summed to form the summary matrix, on which a second round of dynamic programming is performed. (Image: Opabinia regalis, Public domain)

SSAP stands for Sequential Structure Alignment Program. SSAP method uses double dynamic programming to produce structural alignment based on atom to atom vectors in structure space. SSAP constructs the vectors using the beta carbons for all residues by glycine, instead of the alpha carbons typically used, which thus takes into account the rotameric state of each residue and its location along the backbone. SSAP first constructs a series of inter-residue distance vectors between each residue and its nearest non-contiguous neighbors on each protein. A series of matrices is then constructed containing the vector differences between neighbors for each pair of residues for which the vectors were constructed. Using dynamic programming on each resulting matrix determines a series of optimal local alignments, which are then mixed together into a "summary" matrix to which dynamic programming is again used to determine overall structural alignment.
SSAP originally gave only pairwise alignments, but can now provide multiple alignments. It has been used to produce a hierarchical fold classification known as CATH (Class, Architecture, Topology, Homology) through an all-to-all comparison of proteins. This has then been used to put together a CATH protein structure classification database. The constructed database can found here.

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