A　holistic　protein-protein　molecular　docking　approach,　HoDock,　was　established,　composed　of　such　steps　as　binding　site　prediction,　initial　complex　structure　sampling,　refined　complex　structure　sampling,　structure　clustering,　scoring　and　final　structure　selection.　This　article　explains　the　detailed　steps　and　applications　for　CAPRI　Target　39.　The　CAPRI　result　showed　that　three　predicted　binding　site　residues,　A191HIS,　B512ARG　and　B531ARG,　were　correct,　and　there　were　five　submitted　structures　with　a　high　fraction　of　correct　receptor-ligand　interface　residues,　indicating　that　this　docking　approach　may　improve　prediction　accuracy　for　protein-protein　complex　structures.