[AMBER] modeling flexible loops in protein-DNA complexes

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Fri, 12 Aug 2016 10:43:23 +0200

Dear all,

I know this is a little out of topic for the AMBER list, but I would
like to ask whether anybody has experience with building flexible loops
(not visible in the structures) in protein-DNA complexes (loops that do
not necessarily interact with DNA). I played quite a bit with Modeller
but I have the impression that their loop modeling procedures build too
much helical content in these loops. Does anybody have good experiences
with other software/approaches ?

Thanks a lot for any hints

Best wishes
Vlad

-- 
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Fri Aug 12 2016 - 02:00:03 PDT