Energy minimization plays an important role in structure determination and analysis of proteins, peptides and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently Morales and Nocedal have developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computational Optimization and Applications (2002) 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein Ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant ε=1 and a distance dependent dielectric function ε=2r, where r is the distance between two atoms. It is shown that for the optimal parameters, the hybrid approach is typically 2 times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the non-linearity of the energy function is enhanced, i.e., in going from ε=2r to ε=1, where the electrostatic interactions are stronger. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial and error calculations for each problem.