Prediction of Structures of Globular Proteins I. Secondary Structure

抄録

Statistical mechanical method is proposed to predict the secondary structures of globular proteins. Three-state prediction which provides simultaneously the probabilities of α-helix, β-strand and coil is performed with a recurrence method. The probabilities of the ith residue in a-helix or in β-strand are calculated with statistical weights for amino acid pairs in a-helix or in β-strand. We determine the statistical weights to yield the correct predictions for the proteins with known structures instead of calculating directly the interaction energies between residues. To do this, we introduce an objective function and estimate the weights so as to minimize this function by referring to the proteins for optimization. This method yields prediction accuracy of 67% for 13 proteins for accuracy estimation. This value does not exceed the best values obtained by the method based on homology. However, we have a hope to improve the accuracy, since we can analyze the reasons for poor accuracy in contrast to other methods.