There are several online tools and severs for docking studies. You may choose AutoDock or HexDock and manual for these tools is also freely available. 

go through these articles and portals

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151162/

http://link.springer.com/protocol/10.1007%2F978-1-59745-177-2_19

http://sebastianraschka.com/Articles/2014_autodock_energycomps.html

The best freely available software moloecular docking (protein-ligand) is autodock and u can download it from:

 http://mgltools.scripps.edu/

This is a paper about the Hex docking algorithm. 

http://www.loria.fr/~ritchied/papers/ritchie_kemp_psfg_2000.pdf

I use the Hex protein docking server for simple problems.

http://hexserver.loria.fr/hex_server.php

- Reviews:

http://onlinelibrary.wiley.com/doi/10.1002/jmr.2471/abstract

http://pubs.acs.org/doi/abs/10.1021/ci400040d

http://link.springer.com/article/10.1007/s12551-013-0130-2

http://www.ncbi.nlm.nih.gov/pubmed/23531220

- Docking Servers

DockThor - http://www.dockthor.lncc.br/

Docking Server - http://www.dockingserver.com/web/docking/

- Docking Programs

AutoDock Vina - http://vina.scripps.edu/

Glide - http://www.schrodinger.com/

There is a list with several docking programs and servers:

 http://www.vls3d.com/index.php/links/chemoinformatics/virtual-screening/structure-based-virtual-screening