Extremal Optimization for protein folding simulations on the lattice

This paper presents a novel guided search strategy Extremal Optimization (EO) with constrained structure for protein folding. In the proposed algorithm, evaluating the fitness of each monomer in an amino-acid sequence is introduced to guide the improvement of the conformation. In addition, a constrained structure is proposed to reduce the complexity of algorithm. We demonstrate that EO can be applied successfully to the protein folding problem. The results show that the algorithm can find the best solutions so far for the listed benchmarks. Within the achieved results, the search converged rapidly and efficiently.

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