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glossary:ssap [2008/09/19 10:52]
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glossary:ssap [2008/09/19 10:54] (current)
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 +{{tag>other}}
 +====== SSAP =======
 +
 +Full name: __Secondary Structure Alignment Program.__ 
 +
 +This secondary structure alignment program uses dynamic programming to align proteins by matching vectors between residues. For each residue in a protein, a local
 +structural environment is defined by a set of inter-atomic vectors. The method
 +matches residues by comparing these structural environments. An important aspect
 +of these environments is that because they are defined independently for each
 +residue, they are rotationally invariant, making their comparison insensitive
 +to the displacement of substructures. This method also allows other residue
 +properties to be included in the comparison, including solvent accessible
 +area and torsional angles (corresponding to degree of burial and secondary
 +structure), thus improving the alignment of remote protein structures. An important
 +advantage of this method is that it is completely automatic. This algorithm is used to
 +cluster structurally similar proteins in the CATH system.
 +
 +===== References =====
 +
 +{{pubmed>long:8411157}}
 +{{pubmed>long:2769748}}
 +{{pubmed>long:2748567}}
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