Cluster Perturbation Simulated Annealing for Protein Folding Problem

Juan Frausto-Solís (UPEMOR, Mexico)

Mishael Sánchez-Pérez (UNAM, Mexico)

Ernesto Liñan-García (UADEC, Mexico)

Juan Paulo Sánchez-Hernández (ITESM Campus Cuernavaca, Mexico)

Manoj Ramachandran (Toc H Institute of Science and Technology, India)

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

Categories: J.0, J.3, J.7