[gmx-users] allosteric effect

[Tsjerk Wassenaar]

Hi Qasim,

Do you assume MWC or KNF like allostery, and conformational based, dynamics
based or mixed?

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars <qasimpars at gmail.com> wrote:

> Dear gmx users,
>
> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> positive allostery. Based on experimental data, the second ligand of
> protein has greater binding affinity than the first ligand. I would like to
> prove the positive allosteric effect of protein by some analyses. But I
> really don't know which analyses helps me to investigate/look into the
> allosteric effect. Could you please suggest me some useful analyses to
> investigate the allosteric effect (except for RMSD, RMSF)? I have
> simulations for singly liganded, doubly liganded and apo state.
>
> Thanks a lot, in advance.
> --
> Qasim Pars
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-- 
Tsjerk A. Wassenaar, Ph.D.