Prediction of secondary structures of proteins using a two-stage method

Protein structure determination and prediction has been a focal research subject in life sciences due to the importance of protein structure in understanding the biological and chemical activities in any organism. The experimental methods used to determine the structures of proteins demand sophisticated equipment and time. In order to overcome the shortcomings of the experimental methods, a host of algorithms aimed at predicting the location of secondary structure elements using statistical and computational methods are developed. However, prediction accuracies of these methods rarely exceeded 70%. In this paper a novel two-stage method to predict the location of secondary structure elements in a protein using the primary structure data only is presented. In the first stage of the proposed method, folding type of a protein is determined using a novel classification model for multi-class problems. The second stage of the method utilizes data available in the Protein Data Bank and determines the possible location of secondary structure elements in a probabilistic search algorithm. It is shown that the average accuracy of the predictions increased to 74.1%.