Anybody know of any software out there that can predict potential interaction sites between two proteins? They have been shown to interact via y2h screens but I have no idea if they would interact on their own in vitro. Before I clone them into a vector and purify them I would like some sort of confirmation that the interaction could occur in the absence of other cellular factors. There are 2 interactions I am looking at. For the one, the structures of both proteins are known. For the other only one structure is known. So, is there software that uses 2 known structures to predict binding sites and (I know this is a long shot), but is there any software around that could predict an interaction based on the sequences only (or one 3D structure and one sequence)?
Thanks Careina
