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.