An Improved Simulated Annealing Algorithm for Optimization of Protein Folding Problem

Abstract

The biological functionality of a protein is determined by its specific native structure. The challenging task of determining the native structure of a protein from its primary sequence is commonly famous under the name of the protein folding problem (PFP). The objective of the PFP problem is to predict the native structure conformation of a given protein based on its primary sequence. Based on the protein folding process, the PFP problem has been defined as a combinatorial optimization problem (CO) with the use of a simplified model to reduce its complexity. Several optimization approaches have been developed to solve PFP in different lattice models, including 2D square and triangular lattices, 3D cubic and triangular lattices. In this paper, we suggest Improved Simulated Annealing (ISA) to solve the problem of PFP, particularly in the square lattice model.