Which online docking tool can be used for protein-protein docking?

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Jeffrey R Brender

HADDOCK has very good integration with experimental constraints, if any are available

http://www.nmr.chem.uu.nl/haddock2.1/

Uttam Pal

You may also check out PatchDock and related programs because they uses a different approach based on shape complementarity. Besides, you can also provide the binding site information if the experimental data is available.

http://bioinfo3d.cs.tau.ac.il/wk/index.php/Servers_%26_Software