Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts

The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C, C alpha, C beta, N, H alpha of H-alpha chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (MC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super secondary structures. (C) 2015 Elsevier Ltd. All rights reserved.