[gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

I want to refine the model for any bad contact if the structure has. This
article support the simulation of any homology model after its creation by
homology modeling approach "
https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract". Do you please
think that there is no need to refine the model via simulation? or the
claim which i do for refinement via simulation, is biased?

Thanks for consideration!

Amir

On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What us the purpose in doing MD on the homology model? That'll tell you
> whether you need a model with the other parts.
>
> Mark
>
> On Thu, 22 Dec 2016 16:51 Amir Zeb <zebamir85 at gmail.com> wrote:
>
> > 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
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