[gmx-users] Homology model refinement

[Mark Abraham]

Hi,

On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb <zebamir85 at gmail.com> wrote:

> Hi Mark,
>
> I want to refine the model for any bad contact if the structure has.


So, do you expect the structure to be stable in the absence of the other
things? That tells you whether you need to attempt refinement with the
other things, or not.

Mark


> 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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