A genetic algorithm with backtracking for protein structure prediction

In this paper, we propose a simple genetic algorithm for finding the optimal conformation of a protein using the three-dimensional square HP model. A backtracking procedure is used to resolve the positional collisions and illegal conformations that occur during the course of genetic search. Backtracking is shown to be a simple and efficient means of collision repair that requires little overhead. Empirical results show that a genetic algorithm using backtracking can obtain the lowest energy structure of an amino acid sequence in fewer energy evaluations than earlier approaches. Categories and Subject Descriptors I.2.8 [Artificial Intelligence]: Problem Solving, Control Methods and Search

• Type: Conference
• Year: 2006
• Where: GECCO
• Authors: Clayton Matthew Johnson, Anitha Katikireddy
• Keywords: Backtracking, GECCO 2006, Genetic Algorithms, Hp Model, Optimization