Autodock and Autodock vina are good for protein-ligand complex

Cluspro is good for protein-protein complex

They are free

Dear Mr. Nandu, I suggest you to take a look at UCSF DOCK (http://dock.compbio.ucsf.edu/) and AutoDock Vina (http://vina.scripps.edu/).

Best regards.

You may want to have a look at this Q&A: https://www.researchgate.net/post/What_is_the_best_free_software_for_QSAR_and_molecular_docking

autodock 

Autodock, IGEMdock

I work in an institution where we have purchased licence for discovery if you are interested in using commercial software also i can help you out in assessing the software  

Audo Dock shall be useful if you know some details about docking basic 3D coordinates and all that

iGEM dock is good if your performing docking for the first time since its more of a GUI and user friendly type

Dear Nandu,

  You can use Auto Dock Vina or UCSF Dock. Both the softwares are good.

All the Best

Autodock Vina is easy to use and freely available. Along with Autodock Vina you will also require MGL tools 1.5.6 and PyMol Molecular graphics system for pre- and post - docking processing respectively.

Autodock Vina with the "flexible residues" option.

Regards,

Juan

There is also online service on

 http://www.swissdock.ch/

Regards,

 Magdalena

Use free autodock vina. It is incredibly good! Regards, Juan

for protein protein, ZDOCK or GRAMMX is good.

Try CRDock  or CDock (free for academics):

http://ub.cbm.uam.es/software/crdock.php?lang=es

AutoDock ;)

AutoDock vina even though its free gives one of the most accurate results

http://vina.scripps.edu/

autodock vina is best. A complete directory of computational software and server is given in the following link

http://www.click2drug.org/index.html

For the first time users iGEM DOCK is good it s fully GUI and automated too