For protein-protein docking I would suggest HEX. The only problem is sufficeint memory.

With regards

Bruno Sopko

http://hex.loria.fr/

There are several high quality protein-protein docking services, such as HADDOCK, ClusPro, ZDock, GRAMM-X etc. All of the above web servers are free of charge (HADDOCK ClusPro and ZDock require registration) and have been highly used and cited in multiple publications. Check the CAPRI assessment (http://en.wikipedia.org/wiki/Critical_Assessment_of_Prediction_of_Interactions), these tools are almost always on the top of the list, which means they are some of the best docking services to be found.

Hex is also a good and free solution. For protein-ligand docking, I would suggest AutoDock - and the complete MGL Tools suite in general, which is filled with molecular modeling tools, including its own molecular viewer. SwissDock is also free as a web service (its offline version requires CHARMM), and is considered to be a good docking algorithm.

As for publicaton quality images, the matter is simple. Energy outputs, graphs and analysis statistics aside, the result of a docking run is, essentially, a PDB model. Therefore, any PDB viewer can used to visualize and obtain images, and there are many free and high quality solutions (RasMol. UCSF Chimera, VMD, PMV etc). Note that the PyMOL source code is also free (therefore, you can build PyMOL yourself, using just Python and NumPy without paying anything).

In addition to the servers listed above I suggest 

SwarmDock

http://bmm.cancerresearchuk.org/~SwarmDock/

Hex

http://hexserver.loria.fr/

I will suggest you to go for AutoDock 4.2/ AutoDock Vina because it is free software and easy to install and use in any OS (Linux,Windows,iOS). You will learn on your own about the docking and parameter and grid box setting especially for protein-ligand docking. As mentioned by our friend Fotis Baltoumas, MGLTool will aid you.

For protein - protein docking, go for HADDOCK /Cluspro.

I  suggest for you this softwares from my experience as beginner in using those softwares. 

For image rendering for publication, you can use VMD or PyMol. Both softwares can produce a good publication quality images.

I would suggest you to use Adobe photoshop software if you want to  edit your images.

for Small molecule docking Prefer....AutoDock and USF Dock.

for Macromolecule docking.....Haddock is best one, which can be use as webserver and also downloadable, only to linux and Mac users.

Please note that publishing only docking results doesn't have much sense. Thus, the question should be what else/which further steps could be done to improve the quality of research and publish it.

Thanks everyone for your helpful suggestions. 

Dear Rufal i agree with you. 

Dear all, 

If someone please share the stepwise autodock tutorials. I have seen a video on YT but it's not completely understandable. If anyone can share the protocol, i ll be thankful. HEX or Autodock anyone pls do share.

autodock you can prefer for that purpose

I suggest you to use Hex for protein protein docking. Otherwise try using AutoDock. Further you can use Pymol, or Chimera (for better resolution) to take snapshots of the complex which was prepared after dock.

Thanks all for your reply.

Short remark: Haddock only works if you have an idea of your interface and therefore additional constraints (from NMR, mutagenesis or something like this), it will not be able to do a systematic search for possible interfaces .... as far as I understood

autodock, argus lab

AutoDock, iGemDock, Hex, ZDOCK.