If you have a short template structure in polyproline II conformation
and want to have model sequences in the same conformation, just align
them with the template structure and model them in the standard way
with modeller. It does not matter that they are only peptides,
tha target sequence structure will try to reproduce the template
structure.
Andrej
>
> On Mon, 26 Apr 1999, Holger Kremmin wrote:
>
> > Hi,
> > I want to model several short peptides with a special conformation.
> > The templates have the polyproline II conformation, but the model-sequences
> > are far divergent from the template-sequence.
> > How can I model peptides (8-18 aa) with a given conformation ?
> >
>
> Holger,
>
> Could I suggest using CHARMM for this? This type of job is fairly
> easy using that program. I am not sure if there is an easy way in
> modeller unless you have a good understanding of the restraint
> set-up in modeller,
>
> Tony Pemberton
>
> *********************************************************************
> Mr. A.J.Pemberton Tel: +121-414-3388
> c/o Dept. Rheumatology, Fax: +121-414-3982
> Medical School, E-mail:
> The University of Birmingham,
> Birmingham B15 2TT.
> U.K.
> *********************************************************************
>
--
--
Andrej Sali, Assistant Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org