Hello John,
You can include covalently modified residues in your sequence prior to
the model building: i.e. you need to edit your seq alignment.
For the current list of residue types (about 30 "active" and 140
defined) please consult the
$MODINSTALL6v2/modlib/retyp.lib file.
More details about it and about defining new residues:
http://salilab.org/modeller/manual/node29.html
questions: 17, 18
best wishes,
Andras
J Simms wrote:
>
> Hi All,
> I have just started modelling a G Protein-Coupled Receptor,
> which has a number of post translational modifications. My
> problem is that my template, Rhodopsin, is glycosylated on the
> extracellular loops at a different position to my target sequence.
> Is there a way of adding the glycosylation to my target protein
> either at the alignment stage or before the model in refined.
> As always many thanks in advance.
>
> John.
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras