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　(DeltaE(ele)+DeltaG(ACE)+DeltaE(vdw))　had　much　more　potentiality　in　distinguishing　the　near-native　conformations　from　the　incorrect　ones　compared　with　other　scoring　functions,　such　as　DeltaE(ele),　DeltaG(ACE),　DeltaE(ele)+DeltaG(ACE),　DeltaE(ele)+DeltaE(vdw)　and　DeltaG(ACE)+DeltaE(vdw).　It　was　found　that　energy　minimization　could　improve　the　discrimination　results　for　all　the　scoring　functions　mentioned　above　to　some　extent,　especially　for　DeltaE(ele)+DeltaG(ACE)+DeltaE(vdw).　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.