Protein docking Software: ZDOCK
In protein docking, the structure of a complex between two proteins is predicted based on the independently crystallized structures of the components.
ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK (in a more detailed fashion than the calculations performed by ZDOCK).
For basic information on running ZDOCK, see this site.