[gmx-users] delta G of binding for protein-ligand complex
jalemkul at vt.edu
Fri Oct 12 15:43:59 CEST 2012
On 10/12/12 5:44 AM, Archana Sonawani wrote:
> Dear Gromacs Users,
> I have two large organic compounds and one peptidomimetic binding to same
> receptor protein. I want to compare the delatG of binding of all the three
> complexes to show that peptidomimetic binds with greater affinity to
> protein. According to the gromacs tutorial, I have to perform (de)coupling
> of the ligand in complex with the receptor and in bulk solution. I don't
> know exactly how to start with this process.
There is tons of literature on this topic. The protocol is basically the same
for performing decoupling in the receptor and in solvent; the only thing that
differs is the environment.
> Do I need only the protein-ligand complex simulated for 5ns to start with?
Starting with an equilibrated structure of the protein-ligand complex is
necessary, but it's not the only thing you need to do. That's only half of the
free energy calculation; the other half is done just in a box of water. Again,
refer to the literature and review articles on free energy methodology.
Another applicable technique is umbrella sampling, though it is likely to be
more computationally expensive.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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