Protein folding with cellular automata in the 3D HP model
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
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The paper presents an approach to optimize the protein 3D HP model conformation with ant colony Optimisation (ACO). A rapid coordinate system transfer matrix according to the "right hand" rule we defined is used to reduce the computing time. A new scheme to solve the problem of folding deadlock is suggested. During the update of pheromone, a new update method with dynamic pheromone is given and three local search method are provided. Using these method, 3D conformation of standard test sequences with very low energy was found.