Likely the loop needs to be modeled because it is too mobile to
be measured. To observe this, you could run a quick vacuum dynamics
with all but loop frozen, starting from different predictions. I suspect
the same conformational space might be covered. You could even 'draw in'
the missing residues in xleap (not recommended) and get similar space.
Bill
Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Modeller is also an option .. Though I would advise starting simulations
> with different conformations of that loop to ensure that the loop does
> not affect your results.
> If the answers to your question depend on the loop conformations, I
> would be very careful with the interpretations ..
>
> I hope this helps
> Vlad
>
>
> On 09/04/2013 06:08 PM, Wong, Sergio E. wrote:
> > Hi;
> >
> > You can build a loop this size using a program called PLOP. The link is below:
> >
> > http://www.jacobsonlab.org/plop_manual/plop_overview.htm
> >
> > Good luck;
> >
> > -Sergio Wong
> > Biosciences and Biotechnology Division
> > Lawrence Livermore National Laboratory
> > ________________________________________
> > From: Fabian Glaser [fglaser.technion.ac.il]
> > Sent: Tuesday, September 03, 2013 7:05 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] missing loop
> >
> > Hi,
> >
> > I am interest in using amber to study the protein in PDB 3cio. But it has a 12 aa loop missing, which cannot be modeled using similar structures. I wonder what would be the best strategy to model this loop, or alternatively how to simulate this protein dynamics.
> >
> > Thanks a lot,
> >
> > Fabian Glaser,
> > Technion, Israel
> >
> >
> >
> >
> > _______________________________
> > Fabian Glaser, PhD
> > Bioinformatics Knowledge Unit,
> > The Lorry I. Lokey Interdisciplinary
> > Center for Life Sciences and Engineering
> >
> > Technion - Israel Institute of Technology
> > Haifa 32000, ISRAEL
> > fglaser.technion.ac.il
> > Tel: +972 4 8293701
> > Fax: +972 4 8225153
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 09 2013 - 21:00:05 PDT
