Protein Structure Similarity Comparison Using Fast Fourier Transform

The comparison of protein structure similarity is a research focus in bioinformatics, and it plays a very important role in the field of protein structure prediction, protein function prediction and the exploration of protein evolution relationship. In recent years, there were many protein three-dimension structure similarity comparison methods. In this paper, many existing methods of protein three-dimension structure similarity comparison are introduced. And the advantages and disadvantages of various methods are analyzed. Base on the method of using the Cα-Cαmatrix to compare protein structure similarity, a new method is proposed. Information of Cα-Cαdistance matrixes have been transformed to frequency information by Fast Fourier Transform. The similarity of two proteins can be compared by analyzing the frequency information. This method is independent on any sequence information, and can quickly compare and classify protein structures. Experimental results show that the method can be used as effective auxiliary means of protein structure similarity comparison and classification.