An assessment of protein secondary structure prediction methods based on amino acid sequence

Abstract

Five of the several secondary structure prediction methods based on protein amino acid sequence have been computerized, allowing the calculation of joint prediction histograms which have been shown to be superior to any individual prediction. The known structures of about 40 proteins experimentally determined by X-ray crystallography are compared with the predictions resulting from calculated histograms. The accuracy of the predictions for helices is generally much better than for both β-sheet regions and for turns. The overall agreement between prediction and observation within the amino terminal half of the protein molecules is clearly superior to that for the carboxyl half, suggesting an amino nucleating core. Predictions for smaller proteins and thermally stable proteins are generally good, indicating the sensitivity of the methods to short-range but not long-range interactions. In less than half the cases tested were the predictions useful; there was no way of knowing ahead of time if a favorable prediction would result. Given the lack of dramatic improvement with an increase in data base for the schemes and the generally poor agreement factors, it appears that a perfect predictive algorithm must include a consideration of energy minimization, thermalization, and long-range interactions. Extreme caution is suggested in applying present prediction routines to unknown protein structures.