Title: An interval-based algorithm to represent conformational states of experimentally determined polypeptide templates and fast prediction of approximated 3D protein structures

Authors: Márcio Dorn; Osmar Norberto de Souza

Addresses: 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; Institute of Informatics, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 67, Sala 202 91501-970 – Porto Alegre – RS – Brasil ' 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

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 structures; protein structure prediction; interval arithmetic; pattern recognition; data mining; approximate 3D structures; polypeptides.

DOI: 10.1504/IJBRA.2013.056075

International Journal of Bioinformatics Research and Applications, 2013 Vol.9 No.5, pp.462 - 486

Received: 03 Feb 2011
Accepted: 06 Apr 2011
Published online: 18 Sep 2014 *

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