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This work describes a Hierarchical Parallel Genetic Algorithm (HPGA) applied to the Protein Folding Problem (PFP). The modeling of the problem, using the 3DHP-Side-chain model, and details of the HPGA are presented. The effect of the energy weights in the performance of the algorithm was also studied. The HPGA was tested using three sets of benchmark sequences. Results show that the HPGA obtained biologically coherent results, suggesting the adequacy and efficiency of the HPGA for the problem.