[gmx-users] Homology model refinement

[Mijiddorj Batsaikhan]

Hi,

What is your target structure size? If you want to perform explicit solvent
simulation for bigger protein, it may be time-consuming simulation.
My suggestion is that you can run simulation implicitly, it helps you
remove some bad contacts. Then, you can make cluster analysis and find
dominating configurations from section that converged to stable rmsd
values.

Mijiddorj

> > Hello,
> > >
> > > I have created a homology model for a protein, where the seq. identity
> > > between the template and target is 40%. The template structure also
> > > contains co-factor and an inhibitor in bound form means it is a
> complex.
> > > I'll have to define the ligand binding site in target (homology model)
> > > based on inhibitor bound in template structure. But before to reach
> that
> > > stage, i want to simulate the created model to refine the structure
> which
> > > is a common practice in modelling. I'm not pretty sure that should i
> > > simulate the model structure along with the inhibitor and co-factor
> from
> > > template, or one of them, or just only the protein structure alone?
> > Please
> > > let me, if you have any referenced answer.
> > >
> > > Regards
> > >
> > > Amir
> > > --
>
>