Why the Chou-Fasman parameters are not reliable in protein secondary structure prediction Keywords: Chou-Fasman parameters / Protein prediction / Secondary structure

The Chou-Fasman method has been a widely used method for protein secondary structure prediction. This method is based on knowledge about amino acid residues potential to form αhelical regions or β-sheet regions in proteins. Our main interest in this study was to examine the reliability of these Chou-Fasman parameters. We have calculated the Chou-Fasman parameters, with 95% confidence limits, out of 144 non-homologous proteins consisting of 155 chains, and a total of 33118 amino acid residues. All protein chains are X-RAY structures known at a resolution of at least 2.5 Å. We have compared the results of our calculations to those previously done by Chou and Fasman for 15 and 64 proteins. The comparisons show that Chou and Fasman classified four amino acid residues totally wrong in α-helical regions and one in βsheet regions. This is so, because not even the confidence limits we calculated includes the former values determined by Chou and Fasman. Moreover, the confidence limits calculations contradicts most of the Chou and Fasman former amino acid residues classifications.