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Any protein is a linear chain of amino acid, and under specific conditions it folds into a unique native three-dimensional structure. Based upon thermodynamical hypothesis, the native structure of a protein always achieves the global minimum of free energy. The hydrophobic-hydrophilic model for predicting the protein native structure is perhaps one of the most successful and best-studied models. The protein folding problem in the hydrophobic-hydrophilic (HP) model has been proved as an NP-complete problem. This paper is the first one in which we demonstrate that bio-molecular operations with basic logical operations can be used to solve the three dimensional protein folding problem in the HP model. In order to achieve the goal, intelligent bioinformatics logic algorithms are proposed.