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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Received on Wed Sep 04 2013 - 09:30:02 PDT
