> It depends on what you want to learn. If you're looking to confirm your
> suspicions about how a ligand docks in your protein, then adding a restraint
> to force the ligand to adopt the position you expect hardly constitutes
> evidence that the ligand binds that way.
However it might help you decide if such binding is possible, so
I don't think it's a wrong move to try. E.g. you could equilibrate
with the restraints in place, then drop them and see if the ligand
stays put.
Bill
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Received on Wed Jun 02 2010 - 10:30:05 PDT
