AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ, J Comput Chem, 2009 Dec - link

Protein-ligand docking with multiple flexible side chains.
Zhao Y, Sanner MF, J Comput Aided Mol Des, 2008 Sep - link

FLIPDock: docking flexible ligands into flexible receptors.
Zhao Y, Sanner MF, Proteins, 2007 Aug 15 - link

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.
Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS, Proteins, 2002 Jan 1 - link