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The protein is the main working machine of the cells. It has various catalytic and physiological functions. Its function comes from the conformation of the protein and catalytic activity. The conformation is formed by the permutations of amino-acids, and the permutation of the amino-acids, accomplishes the multiplicity of the protein. A great challenge in computational molecular biology is to predicate the protein native structure from its primary amino acid sequence. It is not difficult to obtain protein sequences. However to determine protein structure is not an easy task by current technologies. There is a large gap between them. Therefore, more research is needed to fill the gap. This study proposed a memetic algorithm for protein structure prediction in FCC lattice HP model. The experiment result shows that the MA method proposed in this study can retain the merits of the Genetic algorithm which is good at solve combinatorial problem. It can also increase the efficacy effectively.