Genetic-Annealing Algorithm for 3D Off-lattice Protein Folding Model

Abstract

This paper presents a model used to deal with three-dimensional off-lattice AB protein folding. The model is extended from genetic-annealing algorithm that is for the two-dimensional off-lattice AB protein model. The three-dimensional model also has only two types of residues, hydrophobic and hydrophilic. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem. Also, in contrast to earlier studies using off-lattice AB models, our results demonstrate that the proposed methods are very promising for searching the ground states of protein folding in three dimensions.