Analytically Tuned Simulated Annealing Applied to the Protein Folding Problem

  • Juan Frausto-Solis
  • E. F. Román
  • David Romero
  • Xavier Soberon
  • Ernesto Liñán-García
Conference paper

DOI: 10.1007/978-3-540-72586-2_53

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4488)
Cite this paper as:
Frausto-Solis J., Román E.F., Romero D., Soberon X., Liñán-García E. (2007) Analytically Tuned Simulated Annealing Applied to the Protein Folding Problem. In: Shi Y., van Albada G.D., Dongarra J., Sloot P.M.A. (eds) Computational Science – ICCS 2007. ICCS 2007. Lecture Notes in Computer Science, vol 4488. Springer, Berlin, Heidelberg

Abstract

In this paper a Simulated Annealing algorithm (SA) for solving the Protein Folding Problem (PFP) is presented. This algorithm has two phases: quenching and annealing. The first phase is applied at very high temperatures and the annealing phase is applied at high and low temperatures. The temperature during the quenching phase is decreased by an exponential function. We run through an efficient analytical method to tune the algorithm parameters. This method allows the change of the temperature in accordance with solution quality, which can save large amounts of execution time for PFP.

Keywords

Peptide Protein Folding Simulated Annealing 

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Juan Frausto-Solis
    • 1
  • E. F. Román
    • 1
  • David Romero
    • 2
  • Xavier Soberon
    • 3
  • Ernesto Liñán-García
    • 4
  1. 1.ITESM Campus Cuernavaca, Paseo de la Reforma 182-A Col. Lomas de Cuernavaca, 62589, Temixco MorelosMéxico
  2. 2.IMASS UNAM 
  3. 3.IBT UNAM 
  4. 4.Universidad Autónoma de Coahuila 

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