Re: Modelling post trans mods

[Andras Fiser <andras AT viol.rockefeller.edu>]

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:fisera AT rockefeller.edu
New York, NY 10021-6399, USA # http://salilab.org/~andras