A NSGA-II algorithm for the residue-residue contact prediction

Authors:
Alfonso E. Márquez-Chamorro;Federico Divina;Jesús S. Aguilar-Ruiz;Jaume Bacardit;Gualberto Asencio-Cortés;Cosme E. Santiesteban-Toca
Affiliations:
School of Engineering, Pablo de Olavide University of Sevilla, Spain;School of Engineering, Pablo de Olavide University of Sevilla, Spain;School of Engineering, Pablo de Olavide University of Sevilla, Spain;School of Computer Science, University of Nottingham, United Kingdom;School of Engineering, Pablo de Olavide University of Sevilla, Spain;Centro de Bioplantas, University of Ciego de Avila, Cuba
Venue:
EvoBIO'12 Proceedings of the 10th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Year:
2012

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Abstract

We present a multi-objective evolutionary approach to predict protein contact maps. The algorithm provides a set of rules, inferring whether there is contact between a pair of residues or not. Such rules are based on a set of specific amino acid properties. These properties determine the particular features of each amino acid represented in the rules. In order to test the validity of our proposal, we have compared results obtained by our method with results obtained by other classification methods. The algorithm shows better accuracy and coverage rates than other contact map predictor algorithms. A statistical analysis of the resulting rules was also performed in order to extract conclusions of the protein folding problem.