Chapter

Evolutionary Computation,Machine Learning and Data Mining in Bioinformatics

Volume 4447 of the series Lecture Notes in Computer Science pp 247-257

The Role of a Priori Information in the Minimization of Contact Potentials by Means of Estimation of Distribution Algorithms

  • Roberto SantanaAffiliated withDepartment of Computer Science and Artificial Intelligence University of the Basque Country, Donostia-San Sebastian
  • , Pedro LarrañagaAffiliated withDepartment of Computer Science and Artificial Intelligence University of the Basque Country, Donostia-San Sebastian
  • , Jose A. LozanoAffiliated withDepartment of Computer Science and Artificial Intelligence University of the Basque Country, Donostia-San Sebastian

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Abstract

Directed search methods and probabilistic approaches have been used as two alternative ways for computational protein design. This paper presents a hybrid methodology that combines features from both approaches. Three estimation of distribution algorithms are applied to the solution of a protein design problem by minimization of contact potentials. The combination of probabilistic models able to represent probabilistic dependencies with the use of information about residues interactions in the protein contact graph is shown to improve the efficiency of search for the problems evaluated.

Keywords

estimation of distribution algorithm protein design energy minimization algorithms.