[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

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
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Received on Fri Aug 12 2016 - 02:00:03 PDT
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