Quantum mechanical computations of proteins based on the molecular fragment approach have been carried out, and polarized protein-specific charges have been derived to provide accurate electrostatic interactions for a benchmark set of proteins. Our study shows that, under the polarized protein-specific force field, the native structure indeed corresponds to the lowest-energy conformation for these proteins. In contrast, when a standard mean-field force field such as AMBER is used, the energies of many decoy structures of proteins could be lower than those of the native structures. Furthermore, MD simulations were carried out and verified that the native structures of these proteins not only are statically more stable but are also dynamically more stable under the polarized protein-specific force field. The present results, together with several recent studies, provide strong evidence that protein polarization is critical to stabilizing the native structures of proteins.