Short-Range interactions and decision tree-based protein contact map predictor

Authors:
Cosme E. Santiesteban-Toca;Gualberto Asencio-Cortés;Alfonso E. Márquez-Chamorro;Jesús 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'12 Proceedings of the 10th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Year:
2012

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Abstract

In this paper, we focus on protein contact map prediction, one of the most important intermediate steps of the protein folding problem. The objective of this research is to know how short-range interactions can contribute to a system based on decision trees to learn about the correlation among the covalent structures of a protein residues. We propose a solution to predict protein contact maps that combines the use of decision trees with a new input codification for short-range interactions. The method's performance was very satisfactory, improving the accuracy instead using all information of the protein sequence. For a globulin data set the method can predict contacts with a maximal accuracy of 43%. The presented predictive model illustrates that short-range interactions play the predominant role in determining protein structure.