462 Int. J. Bioinformatics Research and Applications, Vol. 9, No. 5, 2013 An interval-based algorithm to represent conformational states of experimentally determined polypeptide templates and fast prediction of approximated 3D protein structures Márcio Dorn LABIO, PPGCC, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681, Prédio 32, Sala 602 90619-900 – Porto Alegre – RS – Brasil and Institute of Informatics, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 67, Sala 202 91501-970 – Porto Alegre – RS – Brasil E-mail: marcio.dorn@acm.org Osmar Norberto de Souza ∗ LABIO, PPGCC, Faculdade de Informática, Pontifícia UniversidadeCatólica do Rio Grande do Sul, Av. Ipiranga, 6681, Prédio 32, Sala 602 90619-900 – Porto Alegre – RS – Brasil E-mail: osmar.norberto@pucrs.br *Corresponding author Abstract: Predicting the three-dimensional (3-D) structure of a protein that has no templates in the Protein Data Bank (PDB) is a very hard, still an impossible task. Computational prediction methods have been developed during the last years, but the problem still remains challenging. In this paper we present a new strategy based on Interval Arithmetic to store structural information obtained from experimental protein templates and predict native-like approximate three-dimensional structures of proteins. Our objective is to perform the prediction in a very fast manner and predict native-like structures that can be used as starting point structures to ab initio methods. We illustrate the efficacy of our method in five case studies of polypeptides. Keywords: structural bioinformatics; 3-D protein structure prediction; interval arithmetic; pattern recognition; data mining. Copyright © 2013 Inderscience Enterprises Ltd.