blind docking of large protein molecules

 I am interested in investigating potential dockings between protein molecules
 and only have pretty limited ideas about potential binding sites.
 I have toyed with autodock, zdock and hex with mixed results and am
 finding it a bit intensive resources wise. What packages or combinations
 there of do people recommend for this sort of thing?
 Since it does not seem feasible attempt to use both molecules
 in their entirety, I was thinking about splitting one into smaller
 chunks, ie grabbing chunks that are close to the surface and attempting
 to dock them in turn.
 Does anyone have any experience or tips from similar efforts or know of
 any papers etc detailing any efforts or methodologies that I might find
 Thanks in advance!
 Alex Sutcliffe