A decision tree-based method for protein contact map prediction

Authors:
Cosme Ernesto Santiesteban Toca;Alfonso E. Márquez Chamorro;Gualberto Asencio Cortés;Jesus S. Aguilar-Ruiz
Affiliations:
Centro de Bioplantas, University of Ciego de Ávila, Cuba;University of Pablo de Olavide, Sevilla, Spain;University of Pablo de Olavide, Sevilla, Spain;University of Pablo de Olavide, Sevilla, Spain
Venue:
EvoBIO'11 Proceedings of the 9th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Year:
2011

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Abstract

In this paper, we focus on protein contact map prediction. We describe a method where contact maps are predicted using decision tree-based model. The algorithm includes the subsequence information between the couple of analyzed amino acids. In order to evaluate the method generalization capabilities, we carry out an experiment using 173 non-homologous proteins of known structures. Our results indicate that the method can assign protein contacts with an average accuracy of 0.34, superior to the 0.25 obtained by the FNETCSS method. This shows that our algorithm improves the accuracy with respect to the methods compared, especially with the increase of protein length.