Re: [AMBER] missing loop

From: Wong, Sergio E. <>
Date: Wed, 4 Sep 2013 16:08:38 +0000


   You can build a loop this size using a program called PLOP. The link is below:

Good luck;

-Sergio Wong
Biosciences and Biotechnology Division
Lawrence Livermore National Laboratory
From: Fabian Glaser []
Sent: Tuesday, September 03, 2013 7:05 AM
To: AMBER Mailing List
Subject: [AMBER] missing loop


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
Tel: +972 4 8293701
Fax: +972 4 8225153

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