Extremal optimization for the 3D protein folding based on the lattice model

Much of the previous work in the protein field focused on the 2D protein folding due to its simplicity but ignored the 3D protein folding problem. In this paper, based on the work of 2D protein folding problem by primary extremal optimization (EO) algorithm, we study the more complicated 3D protein folding problem with its variation (τ-EO) for the first time. The parameter τ is set as a random value near a constant in each iteration. For the protein with not too long sequence, the experimental results show that the proposed EO algorithm is very efficient.