Thanks, Dr. Case, for the comments. Just to make myself sure, it is
sensible to use TI to study binding affinity differences between a
native and a mutated enzyme to one single ligand *AND* it is sensible to
use a thermodynamic cycle like the one in tutorial A9 with recpetor and
ligand roles swapped (so alchemical mutation of, say, the native to the
mutated one - more specifically, the atoms of the mutated residue that
are either different or have different charges).
Concerning "often done", I must be missing something here because I
made a number of Google searches but did not find properly. Probably I
was not clever enough, so should someone have a specific reference to
point, I would be thankful.
Jorge
> On Mon, Sep 26, 2011, Jorge Iulek wrote:
>> I wonder whether it might be sensible to calculate a delta(deltaG)
>> of a protein mutated (compared to the native one) to bind to a certain
>> ligand through thermodynamic integration. The set up I imagine closest
>> is the one at tutorial A9, but with receptor and ligand roles inverted.
>> Is this sensible?
> It is indeed sensible, and often done.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 27 2011 - 09:30:05 PDT
