Dear All,
I built 200 tetrameric models of my protein using 2 templates. I selected best model as the one having the least DOPE score. On ssessing the stereochemical quality of the model, I found that it had 28 outliers residues (phi, psi), that were lying in disallowed regions of Ramachandran plot. Most of these residues are functionally important and hence can not be ignored. Will it be fine to select each of these residues and model them using loop modelling?
Or can anyone please suggest me some other (better) way of fixing such bad residues?
With Regards
Ruchi
Hii Ruchi!! well.. you can do loop refinement for further refining process. and another thing you can use minimization techniques like MD, where you can give a slight heating up of protein to shake the structure a bit, and then let it relax to attain favorable conformation. Hope it helps.. Cheers! Monika
On Thu, 4 Sep 2008, rsachdeva@imtech.res.in wrote:
> Dear All, > > I built 200 tetrameric models of my protein using 2 templates. I selected best > model as the one having the least DOPE score. On ssessing the stereochemical > quality of the model, I found that it had 28 outliers residues (phi, psi), that > were lying in disallowed regions of Ramachandran plot. Most of these residues > are functionally important and hence can not be ignored. Will it be fine to > select each of these residues and model them using loop modelling? > > Or can anyone please suggest me some other (better) way of fixing such bad > residues? > > With Regards > > Ruchi > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
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mon_sharma＠research.iiit.ac.in -
rsachdeva＠imtech.res.in