Analytically Tuned Simulated Annealing Applied to the Protein Folding Problem

Authors:
Juan Frausto-Solis;E. F. Román;David Romero;Xavier Soberon;Ernesto Liñán-García
Affiliations:
ITESM Campus Cuernavaca, Paseo de la Reforma 182-A Col. Lomas de Cuernavaca, 62589, Temixco Morelos, México;ITESM Campus Cuernavaca, Paseo de la Reforma 182-A Col. Lomas de Cuernavaca, 62589, Temixco Morelos, México;IMASS UNAM,;IBT UNAM,;Universidad Autónoma de Coahuila,
Venue:
ICCS '07 Proceedings of the 7th international conference on Computational Science, Part II
Year:
2007

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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.