A simple method of identifying symmetric substructures of proteins

Accurate identifications of internal symmetric substructures of proteins are needed in protein evolution study and protein design. To overcome the difficulties met by previous methods, here we propose a simple quantitative one by using a similarity matrix plus Pearson's correlation analysis. The distance root-mean-square deviation (dRMSD) is used to measure the similarity of two substructures in a protein. We applied this method to the proteins of the β-propeller, jelly roll, and β-trefoil families and the results show that this method cannot only detect the internal repetitive structures in proteins effectively, but also can identify their locations easily.