Thank you so much for the suggestions, Tomas! Yes, my ligand is a small
molecule. I have the crystal structure of the ligands bound to the protein,
do I still need to computationally dock the ligand to the two pockets, can
I calculate the parameters of binding directly using the crystal structure?

Best,
Wei


On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas <
tomas.malinaus...@gmail.com> wrote:

> Dear Wei Shi,
> is your ligand a small molecule? If it is a small molecule, I would
> try to computationally dock the small molecule to two pockets
> separately using AutoDock, and look at the estimated free energies of
> binding.
> Best wishes,
> Tomas
>
> On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi <wei.shi...@gmail.com> wrote:
> > Hi all,
> > I got the crystal structure of a transcription factor, and every monomer
> > binds two molecules of the same ligand in different binding pockets. And
> I
> > also did the ITC experiment, titrating the ligand into the protein, and
> got
> > a U-shaped curve. The binding affinity for the first binding site is
> higher
> > than the second binding site.
> > I am wondering whether I could computationally determine from the
> > protein-ligand complex structure that which binding site has higher
> affinity
> > for the ligand and correlate the binding sites with the parameters I got
> > from ITC experiment.
> > Thank you so much!
> >
> > Best,
> > Wei
>

Reply via email to