Re: [modeller_usage] modeling of phosphorylated polypeptide
To: Alden Huang <>
Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide
From: Xiao-Ping Zhang <>
Date: Fri, 31 Oct 2008 11:18:11 -0700
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.
At 02:16 AM 10/29/2008, you wrote:
Perhaps homology modelling is not the best method. This might help:
Best of luck.
Xiao-Ping Zhang wrote:
> 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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