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--- glossary:ssap [2008/08/07 14:22] – cuff
+++ glossary:ssap [2008/09/19 10:54] (current) – garner
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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}}

CATH