A filter-and-fan approach to the 2D HP model of the protein folding problem

César Rego (), Haitao Li () and Fred Glover ()

Annals of Operations Research, 2011, vol. 188, issue 1, 389-414

Abstract: We examine a prominent and widely-studied model of the protein folding problem, the two-dimensional (2D) HP model, by means of a filter-and-fan (F&F) solution approach. Our method is designed to generate compound moves that explore the solution space in a dynamic and adaptive fashion. Computational results for standard sets of benchmark problems show that the F&F algorithm is highly competitive with the current leading algorithms, requiring only a single solution trial to obtain best known solutions to all problems tested, in contrast to a hundred or more trials required in the typical case to evaluate the performance of the best of the alternative methods. Copyright Springer Science+Business Media, LLC 2011

Keywords: Metaheuristics; Tabu search; Compound neighborhoods; Filter-and-fan; Protein folding; Bioinformatics (search for similar items in EconPapers)
Date: 2011
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DOI: 10.1007/s10479-009-0666-5

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