[gmx-users] Homology model refinement

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 22 07:09:51 CET 2016


What us the purpose in doing MD on the homology model? That'll tell you
whether you need a model with the other parts.


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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