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Appeared in: 10th Panhellenic Conference on Informatics (PCI 2005), P. Bozanis and E.N. Houstis (Eds.), Springer-Verlag, LNCS 3746, pp. 448-456, Volos, Greece, 11-13 November, 2005.

Abstract: Nowadays, the number of protein sequences being stored in central protein databases from labs all over the world is constantly increasing. From these proteins only a fraction has been experimentally analyzed in order to detect their structure and hence their function in the corresponding organism. The reason is that experimental determination of structure is labor-intensive and quite time-consuming. Therefore there is the need for automated tools that can classify new proteins to structural families. This paper presents a comparative evaluation of several algorithms that learn such classification models from data concerning patterns of proteins with known structure. In addition, several approaches that combine multiple learning algorithms to increase the accuracy of predictions are evaluated. The results of the experiments provide insights that can help biologists and computer scientists design high-performance protein classification systems of high quality

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