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
>
>
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>
> _______________________________________________
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> 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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Received on Wed Sep 04 2013 - 10:00:03 PDT
