Re: [modeller_usage] modeling of phosphorylated polypeptide
Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide
From: Modeller Caretaker <>
Date: Tue, 11 Nov 2008 22:32:20 -0800
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?
Sure - you could build a comparative model in the usual way (assuming
you have a template) and phosphorylate the residues you're interested in
by applying a suitable patch in the special_patches method. If a
suitable patch does not exist, you'll have to add a new one to the
topology file - see the FAQ or the CHARMM forums.
If your intention is to take an existing PDB and use Modeller to
phosphorylate some residues, Modeller is perhaps not the best package
for the job - you'd be better off using a dedicated MD program.
Ben Webb, Modeller Caretaker
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