Evaluation of secondary structure predictions in proteins

Abstract

Data of 33 proteins are used to compare four methods which predict secondary structure from the amino acid sequence. The prediction of alpha-helices according to the histogram method of Argos et al. (Argos, P., Schwarz, J. and Schwarz, J. (1976) Biochim. Biophys. Acta 439, 261-273) is on the average as reliable as the statistical method of Nagano (Nagano, K. (1973) J. Mol. Biol. 75, 401-420). Both methods predict helices more accurately than the stereo-chemical method of Lim (Lim, V.I. (1974) J. Mol. Biol. 88, 873-894). The method of Nagano yields the best prediction of beta-structure, while the beta-structure predictions of Lim and Argos et al. are not significantly different. The results of the alpha-helix and beta-structure predictions according to the statistical mechanical method of Tanaka and Scheraga (Tanaka, S. and Scheraga, H.A. (1976) Macromolecules 9, 168-182) are inferior to those obtained by the other three methods. For the prediction of turns, no significant difference between the methods of Nagano (Nagano, K. (1974) J. Mol. Biol. 84, 337-372) and Argos et al. was found.