A new quantitative criterion to distinguish between alpha/beta and alpha+beta proteins (domains).
According to the statistical analysis, it is shown that the differences of the content of alpha-helix and beta-strand between alpha/beta and alpha+beta proteins are of statistical significance. Based on the secondary structure content and the percentage of parallel or anti-parallel strands, any mixed alphabeta protein can be represented by a point in a three-dimensional prism. The distribution of the mapping points for 79 mixed alphabeta proteins (domains), of which 26 are class alpha/beta and 53 are class alpha+beta, 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 alpha/beta and alpha+beta 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 alpha/beta and alpha+beta 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.
Zhang
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CT
Department of Physics, Tianjin University, China. ctzhang@tju.edu.cn
Zhang
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D000465:Algorithms; D000818:Animals; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D006801:Humans; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D012680:Sensitivity and Specificity
D011506:Proteins