The role of a priori information in the minimization of contact potentials by means of estimation of distribution algorithms

Authors:
Roberto Santana;Pedro Larrañaga;Jose A. Lozano
Affiliations:
Department of Computer Science and Artificial Intelligence, University of the Basque Country, Donostia-San Sebastian, Spain;Department of Computer Science and Artificial Intelligence, University of the Basque Country, Donostia-San Sebastian, Spain;Department of Computer Science and Artificial Intelligence, University of the Basque Country, Donostia-San Sebastian, Spain
Venue:
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Year:
2007

Citing 7
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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.