Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/GANGSTA+

From Wikibooks, open books for an open world
Jump to navigation Jump to search


GANGSTA+ is a combinatorial algorithm for non-sequential structural alignment of proteins and similarity search in databases. This method uses a combinatorial approach on the secondary structural level to find similarities between two protein structures based on contact maps. Different SSE (Secondary Structure Element) assignment modes can be used for this program. This assignment of SSEs can be performed with respect to the sequential order of SSEs in the polypeptide chain of the considered protein pair (sequential alignment), or by ignoring this order completely (non-sequential alignment). SSE pairs can also be aligned in reverse orientation if desired. The highest ranking SSE assignments are transferred to the residue level by a point matching approach. In order to obtain an initial common set of atomic coordinates for both proteins, pairwise attractive interactions of the alpha carbon atom pairs are defined by inverse Lorentzians and the energy is minimized. The GANGSTA+ database can be found here.