A statistical method for predicting alpha-helical and beta-sheet regions in proteins from their amino acidic sequences

Abstract

In this paper we propose a new method to predict the secondary structure of proteins from sequence data. A satisfactory improvement of the available efficiency of prediction is obtained. The described method takes into account the frequency of each pair of amino acids in alpha-helical, beta-sheet and random coil regions according to previous results that the sequences of amino acidic residues in these regions are autocorrelated. The rules of the method are not derived from the analysis of the regions of proteins with a known secondary structure, but they are instead based on statistical considerations. In such a way the obtained value of efficiency of the method (88%) has a high reliability: in fact, it is correct to test a method only on the data not used to construct it. A new definition of efficiency of a predictive method is given to resolve the ambiguities arising from the previously accepted definitions.