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
expand article infoJuan 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
Open Access
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.
simulated annealing, protein folding, tuned SA, cluster perturbation simulated annealing