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Detection of protein complexes and their structures is crucial for understanding the role of protein complexes in the basic biology of organisms. Computational methods can provide researchers with a good starting point for the analysis of protein complexes. However, computational docking methods are often not accurate and their results need to be further refined to improve interface packing. In this paper, we introduce a novel refinement method that incorporates evolutionary information by employing an energy function containing Evolutionary Trace (ET)-based scoring function, which also takes shape complementarity, electrostatic and Van der Waals interactions into account. We tested our method on docked candidates of three protein complexes produced by a separate docking method. Our results suggest that the energy function can help biasing the results towards complexes with native interactions, filtering out false results. Our refinement method is able to produce structures with better RMSDs with respect to the known complexes and lower energies than those initial docked structures.