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 of organisms. The experimental methods used to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 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, the folding type of a protein is determined using a novel classification approach 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 is 74.1 % on a large structure dataset. (C) 2007 Elsevier Ltd. All rights reserved.