I have Protein A, Protein B and a Drug (small molecule). Protein B is an enzyme which can bind to protein A and can hydroxylate it. During docking study, my drug bound to Protein A binding site of Protein B. Now I want to simulate the interaction between these molecules and see whether my Drug will be able prevent the interaction between Protein A & B. For simulation I use Gromacs software.
@Hamed So you are saying that do a protein-protein (A&B) docking in HADDOCK and use the output file to do a protein complex (A&B)-drug simulation?
To test your hypothesis, assuming the ergodicity, you would need to observe multiple binding / unbinding events in your system, which would take several years of calculation on a modern cluster. A more affordable, but still a quite costly way, would be to set up a Free Energy Perturbation simulation, in which you could decouple the ligand from a hypothetic A-ligand-B complex. However, if you don't have an experimental structure of the A-B complex or don't know where exactly the ligand binds, this isn't worth it.
Try this link
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
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