Re: [modeller_usage] modeling of phosphorylated polypeptide

["Dibyabhaba Pradhan" <>]

Respected sir,

I modelled number of proteins by basic modelling. After basic
modelling during procheck evaluation the residues in most favorable
region is generally above 90% but after loop refinement the residues
in most favorable region comes below 90%. Please kindly inform me what
may be the region for this.

Also after energy minimization the the percentage of residue in most
favorable region decreses.

I will be grateful to listen from u regarding my query

Thanking you,

Dibyabhaba Pradhan
Project Assistant, SVIMS BIC, India


On 10/31/08, Xiao-Ping Zhang <> wrote:
> Dear Alden,
>
> Thank you for your reply and your information. My idea is very
> similar to the idea presented in this nice paper. But the the
> approaches they used are beyond the limit of my knowledge. I hope
> some one can implement their results into a public available program
> (for example, Modeller, PyMol or Deep Viewer).
>
> Direct homology modeling of phosphorylated polypeptide may not make
> any sense if the template used is not phosphorylated because the
> conformational change. But if a molecular modeling program allows to
> add the phosphate group on a model (similar to adding S-S bridge in
> Modeller) followed by MD simulation, the final model could make sense
> (Groban et al's paper is very encouraging).
>
> I noticed that in the topological library of Modeller9v4, there are
> information for "converting (patching?) tyrosine to monoanionic
> phosphotyrosine (PRES TP1)", but no information on converting Thr,
> Ser and Asp. I wonder if any body tried to patch a model from
> Tyrosine to phosphotyrosine with Modeller. Is there any possibility
> to implement information for other residues for patching purpose?
>
> Is there any other free program which has this functionality?
>
> Thank you for your comments and suggestions.
>
> Best regards,
>
> Xiao-Ping
>
>
> At 02:16 AM 10/29/2008, you wrote:
> >Perhaps homology modelling is not the best method. This might help:
> >
> >http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440919
> >
> >Best of luck.
> >
> >~alden
> >
> >
> >Xiao-Ping Zhang wrote:
> > > Hi,
> > >
> > > Many proteins are phosphorylated in vivo and and the status of their
> > > phosphorylation correlate to their function. The residues which are
> > > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry.
> > > I wonder how to build a phosphorylated model directly or how to apply a
> > > patch on a model to get a phosphorylated model in Modeller?
> > >
> > > Thank you advance for your suggestions.
> > >
> > > Xiao-Ping Zhang
> > >
> > >
> > >
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> > > https://salilab.org/mailman/listinfo/modeller_usage
> > >
> > >
>
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