Hi, I am a brand new user of Rosetta... I want to model in different substrates in a transporter, and see how the substrates affect the overall protein structure. The problem is, the binding pocket I am trying to look at is pretty much in the center of the protein, so one question is: how can I define a region of the protein where I want my ligand to dock? A confounding variable is that my protein also has a cofactor covalently bound to a residue side chain. A colleague in my lab tried to help me, but we got stuck with this covalently bound cofactor issue. Could someone please give us a strategy of how to deal with the cofactor in the PDB file, as well as how to deal with the docking area being a pocket inside the protein?
Thanks in advance for any help!