[gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

Thanks for your response. I did for simulation for both the systems 1. only
protein 2. protein with co-factor. By the way, I'm not pretty sure, but I'm
relying on rmsd of C-alpha to evaluate the structure's stability. In both
the cases, the rmsd range was highly wide ~3-6 nm. Then i superimposed the
input protein structure and the snapshot from the last frame, so the rmsd
was around 5 angstrom between the two structures.

[image: Inline image 1]

On Wed, Dec 21, 2016 at 10:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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