Autodocksuite is a set of automated docking tools to study protein - ligand interactions which is being developed by folks here.
It's a free software and I have packaged it for Fedora. The latest version of the software is now available in the testing repositories for Fedora 19 and 20.
The developers have provided some excellent documentation which can obtained from following the links below.
They also have a GUI application for analyzing the docking data (which uses the above package in the backend). Unfortunately, it comes with commercial use restriction and hence cannot be included in Fedora.