JUCS - Journal of Universal Computer Science 19(15): 2207-2223, doi: 10.3217/jucs-019-15-2207

Cluster Perturbation Simulated Annealing for Protein Folding Problem

Juan Frausto-Solís^‡, Mishael Sánchez-Pérez^§, Ernesto Liñan-García^|, Juan Paulo Sánchez-Hernández^¶, Manoj Ramachandran^#

‡ UPEMOR, Jiutepec, Mexico§ UNAM, Cuernavaca, Mexico| UADEC, Saltillo, Mexico¶ ITESM Campus Cuernavaca, Jiutepec, Mexico# Toc H Institute of Science and Technology, Ernakulam, India

Corresponding author: Juan Frausto-Solís ( juan.frausto@upemor.edu.mx )

This article is freely available under the J.UCS Open Content License.

Citation: Frausto-Solís J, Sánchez-Pérez M, Liñan-García E, Sánchez-Hernández JP, Ramachandran M (2013) Cluster Perturbation Simulated Annealing for Protein Folding Problem. JUCS - Journal of Universal Computer Science 19(15): 2207-2223. https://doi.org/10.3217/jucs-019-15-2207

Abstract

In this paper, an improved Simulated Annealing algorithm for Protein Folding Problem (PFP) is presented. This algorithm called Cluster Perturbation Simulated Annealing (CPSA) is based on a brand new scheme to generate new solutions using a cluster perturbation. The algorithm is divided into two phases: Cluster Perturbation Phase and the Reheat Phase. The first phase obtains a good solution in a small amount of time, and it is applied at very high temperatures. The second phase starts with a threshold temperature and reheats the system for a better exploration. CPSA reduces the execution time of the Simulated Annealing Algorithm without sacrificing quality to find a native structure in PFP in Ab-Initio approaches.

Keywords

simulated annealing, protein folding, tuned SA, cluster perturbation simulated annealing