Abstract: A scoring function that contains the electrostatic, desolvation and van der Waals energy was used to discriminate the near-native conformations in protein-protein docking. The analysis results of the docked structures for seventeen protein complexes showed that the scoring function including van der Waals energy（ΔEele＋ΔGACE＋ΔEvdw） had much more potentiality in distinguishing the near-native conformations from the incorrect ones compared with other scoring functions, such as ΔEele, ΔGACE, ΔEele＋ΔGACE, ΔEele＋ΔEvdw andΔGACE＋ΔEvdw. It was found that energy minimization could improve the discrimination results for all the scoring functions mentioned above to some extent, especially forΔEele＋ΔGACE＋ΔEvdw. Finally, to further determinate the near-native structure, we performed the molecular dynamics (MD) simulations for the candidate structures of 4INSXX. According to the variations of the mean square deviation (MSD) of the structures in MD trajectories relative to the initial structures, the false structures could be excluded.