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

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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.

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Authors and Affiliations

  1. School of Business Administration, University of Mississippi, Oxford, MS, 38677, USA

    César Rego

  2. College of Business Administration, University of Missouri–St. Louis, One University Blvd., St., Louis, MO, 63121-4400, USA

    Haitao Li

  3. University of Colorado, Boulder, CO, 80309-0419, USA

    Fred Glover

Authors
  1. César Rego
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  2. Haitao Li
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  3. Fred Glover
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Correspondence to César Rego.

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Rego, C., Li, H. & Glover, F. A filter-and-fan approach to the 2D HP model of the protein folding problem. Ann Oper Res 188, 389–414 (2011). https://doi.org/10.1007/s10479-009-0666-5

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