Abstract
A number of methods to predicting the folding type of a protein based on its amino acid composition have been developed during the past few years. In order to perform an objective and fair comparison of different prediction methods, a Monte Carlo simulation method was proposed to calculate the asymptotic limit of the prediction accuracy [Zhang and Chou (1992),Biophys. J. 63, 1523–1529, referred to as simulation method I]. However, simulation method I was based on an oversimplified assumption, i.e., there are no correlations between the compositions of different amino acids. By taking into account such correlations, a new method, referred to as simulation method II, has been proposed to recalculate the objective accuracy of prediction for the least Euclidean distance method [Nakashimaet al. (1986),J. Biochem. 99, 152–162] and the least Minkowski distance method [Chou (1989),Prediction in Protein Structure and the Principles of Protein Conformation, Plenum Press, New York, pp. 549–586], respectively. The results show that the prediction accuracy of the former is still better than that of the latter, as found by simulation method I; however, after incorporating the correlative effect, the objective prediction accuracies become lower for both methods. The reason for this phenomenon is discussed in detail. The simulation method and the idea developed in this paper can be applied to examine any other statistical prediction method, including the computersimulated neural network method.
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References
Chou, K. C. and Zhang, C. T. (1994). Predicting protein folding types by distance functions that make allowances for amino acid interactions.J. Biol. Chem. 269, 22014–22020.
Chou, P. Y. (1980). Amino acid composition of four classes of proteins.Second Chemical Congress of the North American Continent, Las Vegas.
Chou, P. Y. (1989). Prediction of protein structural classes from amino acid composition. InPrediction of Protein Structure and the Principles of Protein Conformation, G. D. Fasman, editor. Plenum Press, New York. 549–586.
DeGroot, M. H. (1986).Probability and Statistics, 2nd ed., Addison-Wesley Publishing Company, Reading, MA. 267–278.
Levitt, M., and C. Chothia (1976). Structural patterns in globular proteins.Nature (Lond.)261, 552–557.
Nakashima, H., K. Nishikawa, and T. Ooi (1986). The folding type of a protein is relevant to the amino acid composition.J. Biochem. 99, 152–162.
Richardson, J. S., and D. C. Richardson (1989). Principles and patterns of protein conformation. InPrediction of Protein Structure and the Principles of Protein conformation. G. D. Fasman, editor. Plenum Press, New York. 1–98.
Zhang, C. T., and Chou, K. C. (1992). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition.Biophys. J. 63, 1523–1529.
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Zhang, CT., Chou, KC. Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. J Protein Chem 14, 251–258 (1995). https://doi.org/10.1007/BF01886766
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DOI: https://doi.org/10.1007/BF01886766