Secondary Structure Guided Superimposition tool (SSGS)

 

Motivation

Secondary structure elements such as a-helices and ß-sheets are hydrogen bonded and fluctuate less than loop regions. Therefore there is a need for a protein pairwise superimposition that is permissive, and allows a loose matching between the compared proteins in loop assigned regions


 

Given two protein fragments SSGS superimposes them while giving a greater weight to superimposing the beta sheet and a-helix assigned residues in an affine mismatch and affine gap manner. The yellow and red colored areas of the proteins show areas that were not matched. In the yellow colored regions, the backbones of the proteins A and B are spatially separated. The red colored area is a gap region in which the residues of protein A were disregarded.