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
