Comparing 3-D protein structures similarity by using fractal features

Abstract

We propose a new method for finding similarity in 3-D protein structure comparison. Different from the other existing methods, our method is grounded in the theory of fractal geometry. The proposed feature vectors of protein structures are simple to implement. The method is very fast because it requires neither alignment of the chains nor any chain-chain comparison. We calculate the fractal features of a set of 200 protein structures selected from PDB(Protein Data Bank). The experimental result shows that our method is very effective in classification of 3-D protein structures.