Improving the Efficiency of MECoMaP: A Protein Residue-Residue Contact Predictor

  • Alfonso E. Márquez Chamorro
  • Federico Divina
  • Jesús S. Aguilar-Ruiz
  • Cosme E. Santiesteban Toca
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8259)

Abstract

This work proposes an improvement of the multi-objective evolutionary method for the protein residue-residue contact prediction called MECoMaP. This method bases its prediction on physico-chemical properties of amino acids, structural features and evolutionary information of the proteins. The evolutionary algorithm produces a set of decision rules that identifies contacts between amino acids. These decision rules generated by the algorithm represent a set of conditions to predict residue-residue contacts. A new encoding used, a fast evaluation of the examples from the training data set and a treatment of unbalanced classes of data were considered to improve the the efficiency of the algorithm.

Keywords

protein structure prediction residue-residue contact multi-objective optimization evolutionary computation 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Alfonso E. Márquez Chamorro
    • 1
  • Federico Divina
    • 1
  • Jesús S. Aguilar-Ruiz
    • 1
  • Cosme E. Santiesteban Toca
    • 2
  1. 1.School of EngineeringPablo de Olavide University of SevillaSpain
  2. 2.Centro de BioplantasUniversity of Ciego de AvilaCuba

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