Hi Wei: Based on the structure, you can calculate the binding surface between the protein and the ligand. Maybe the two binding pockets will give you two different numbers. And the larger one usually can have the higher binding affinity. You also can analyse how the ligand interacts with the protein though hydrophobic or electrostatic interaction , etc? the last, you may also compare the b factors of the ligand or the protein binding pocket regions after you refining the structure. These things may give you some hints about which binding site is more strong.
Dee Date: Mon, 18 Nov 2013 22:45:58 -0500 From: wei.shi...@gmail.com Subject: Re: [ccp4bb] distinguish ligand binding sites within a protein To: CCP4BB@JISCMAIL.AC.UK 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