It appears to me that the question was general even though it was mailed to Modeller-specific list. So no, Modeller can't do protein docking, but yes, protein-protein docking can be done. See links below for more info:
http://en.wikipedia.org/wiki/Protein-protein_docking http://zlab.bu.edu/zdock/dockingsites.shtml
My general advice: whenever in doubt, go to Wikipedia and type few keywords - it comes up with something relevant more often than not.
Cheers,
Mensur
At 10:35 AM 9/4/2007, Modeller Caretaker wrote: >rgerber2@bigred.unl.edu wrote: > > I was wondering if it was possible, given two protein sequences or > > structures, to show possible docking interactions between the two > > proteins? And if so, how this is done?? > >No - Modeller itself does not do any kind of protein-protein docking. > > Ben Webb, Modeller Caretaker
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