The Similarity Comparison of G-Protein Coupled Receptor Based on Structural Matrix Algorithm

Based on the chemical property of amino acids and the related properties of protein secondary structure, 20 amino acids were classified into the following four types: hydrophilic, polar, charged, namely X=HPC={D, N, S, H, T, C}, hydrophobic, nonpolar, namely Z=H A={Y, F, V, I, W, M}, non-polar and small in size, namely B=AS={G, P}, others, namely J=O={R, K, E, A, Q}. With the help of classification, a protein sequence was transformed into a time series through mapping, which used the number of 1, 2, 3, 4 to represent X, Z, B, J respectively and was introduced to describe the structural character of protein sequences. Then a similarity model of the protein sequences was built by the similarity measurement of structural matrix, which was defined according to some characters of structural matrix. At last, 36 kinds of G-protein coupled receptors were analyzed to verify the effectiveness of the proposed method.