Sequential structure alignment program: Difference between revisions

Revision as of 09:44, 21 June 2011

Revision as of 22:05, 12 November 2011

Line 2:

The '''SSAP''' ('''Sequential Structure Alignment Program''') method uses double [[dynamic programming]] to produce a structural alignment based on atom-to-atom [[Vector (geometric)|vectors]] in structure space. Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the [[beta carbon]]s 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.<ref name="taylor">Taylor{{cite WR, Flores TP, Orengo CA. (1994). Multiple protein structure alignment. ''Protein Sci'' 3(10):1858-70.pmid|7849601}}</ref> It has been applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as [[CATH]] (Class, Architecture, Topology, Homology),.<ref name="orengoOrengo1997">{{cite journal |author=Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. (1997) |title=CATH:--a A hierarchicalhierarchic classification of protein ___domain structures. ''|journal=Structure'' |volume=5( |issue=8): 1093-1108|pages=1093–1108 |year=1997 |pmid=9309224 |doi=10.1016/S0969-2126(97)00260-8}}</ref> which has been used to construct the [http://www.cathdb.info/latest/index.html 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<ref name="porwal">Porwal{{cite G, Jain S, Babu SD, Singh D, Nanavati H, Noronha S. (2007) Protein Structure Prediction Aided by Geometrical and Probabilistic Constraints. ''J. Comput. Chem.'' 28(12): 1943-1952.pmid|17450548}}</ref>.

==See also==