A new quantitative criterion to distinguish between α/β and α+β proteins (domains)

Abstract

According to the statistical analysis, it is shown that the differences of the content of α-helix and β-strand between α/β and α+β proteins are of statistical significance. Based on the secondary structure content and the percentage of parallel or anti-parallel strands, any mixed αβ protein can be represented by a point in a three-dimensional prism. The distribution of the mapping points for 79 mixed αβ proteins (domains), of which 26 are class α/β and 53 are class α+β, shows that the two kinds of points are situated at distinct regions roughly. A new quantitative criterion based on the Fisher discriminant algorithm is proposed to distinguish between the α/β and α+β proteins (domains). Of the 79 proteins 77 are correctly classified (97.5%). As a stringent cross-validation test, the jackknife test shows that of the 79 proteins 77 are correctly classified. The jackknife test accuracy is still 97.5%. These figures indicate the self-consistence and the extrapolating effectiveness of the new quantitative criterion. Applying the new criterion to reclassify the α/β and α+β proteins (domains) in SCOP is also discussed. It is hoped that the new quantitative criterion will be useful for the development of protein classification databases.