On Wed, Jun 2, 2010 at 1:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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.
>
That's true, but my point was that in the end, the restraints have to come
off to make any statements about binding conformation, etc. Everybody's
interpretation of an email differs, I suppose... I would agree with Bill's
statement/suggestion.
All the best,
Jason
> Bill
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 02 2010 - 11:00:14 PDT
