This paper presents an approach for deriving 3-D structures of polypeptide chains which have minimum energy. The well-known optimization algorithms are usually applied on the model which contains hard constraints over coordinates of the atoms. The drawback of such strategies is an inefficient search for the optimal solution. Our approach proceeds in two steps: first, the standard model is transformed into an equivalent model without hard constraints, and second, the simulated annealing local search algorithm is performed. The empirical results demonstrate that simulated annealing on the proposed model outperforms traditional search algorithms especially with respect to running times.