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 >