Hi Jason,
Thanks for the reply. Do you have any idea about the literature, where they
have performed MM-PBSA biding free energy calculations for the 1:n
stoichiometry of macromolecule and ligand. Please provide link of the
articles if possible.
On Sun, Nov 17, 2013 at 10:03 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Nov 17, 2013 at 12:03 AM, Vaibhav Jain <jain13.vaibhav.gmail.com
> >wrote:
>
> > Hello everyone !!
> >
> > I am wondering if MM-PBSA approach can be used for calculating the
> binding
> > free energy of a ligand with a macromolecule in the presence of other
> bound
> > identical ligands, which are in close proximity or stacked together.
> >
>
> Sure. How you proceed depends on what you want to learn. You can treat
> one ligand as the 'ligand' and the rest as part of the 'receptor'. You can
> treat all ligands as one collective 'ligand' and the receptor as the
> receptor. The first approach is probably more reliable than the others
> (especially if there is cooperativity in the different binding events
> associated with conformational allostery).
>
> System consisting of hyperbranched polymer in which 7 molecules of same
> > ligand are encapsulated. Now I wish to calculate the binding free energy
> of
> > each of the 7 bound ligand.
> >
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
*Warm Regards *
Vaibhav Jain (Ph.D. Scholar)
Dept. of Pharmacoinformatics
NIPER, S.A.S. Nagar (Punjab)
India, 160 062
Mob no: +91-9988412195
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Received on Mon Nov 18 2013 - 03:30:02 PST
