If you are dealing with oligomers conserved in evolution, InterEvDock can be a
good choice since it implements a coevolution-based score
Their new version handle oligomers with sequence alignments automatically
generated for every subunit.
It performed very well in CAPRI.
Laboratory of Structural Biology and Radiobiology
I2BC (Institute of Integrated Biology of the Cell)
CEA, Saclay, Bât 144, room 140D,
91191 Gif-s-Yvette, FRANCE
phone: +33 (0)1 69 08 76 77