Unreliability of the Chou-Fasman parameters in predicting protein secondary structure.

The Chou-Fasman method has been widely used for predicting protein secondary structure. It is based on knowledge of the potential of amino acid residues to form alpha-helical or beta-sheet regions in proteins. Our main interest in this study was to examine the reliability of these Chou-Fasman parameters. We calculated the Chou-Fasman parameters, with 95% confidence limits, of 144 non-homologous proteins consisting of 155 chains, and a total of 33 118 amino acid residues. All of the protein chains used were X-ray structures known at a resolution of at least 2.5 A. We compared the results of our calculations with those previously done by Chou and Fasman. Our results show that Chou and Fasman classified four amino acid residues wrongly in alpha-helical regions and one in a beta-sheet region. This is so, because the confidence limits we calculated did not include the values determined by Chou and Fasman. Moreover, the confidence limit calculations contradict most of the Chou-Fasman classification of amino acid residues.