Dear Jorge,
recently I saw an interesting paper that might help you to do exactly
what you need: Bioinformatics doi: 10.1093/bioinformatics/bty347.
BW,
Oliviero
On 28.08.2018 15:03, Jorge Iulek wrote:
Dear all,
I am working currently on a structure that, nicely, presents two
different orientations between its domains when one compares monomers
of the tetramer in the asymmetric unit.
I notice, in this nature gift, that a helix, probably central (in
its role) for the relation (orientation) between the two domains,
assumes different relation to other one (helix, that belongs to one of
the domains) such that they are (significantly) more or less
"coiled-coiled"one to another, once the domains are in the "close" or
"open" conformation. We have already analyzed the hydrogen bonds and
salt bridges that are disrupted (or formed) due to the different
(domain and helix) conformations.
I wonder whether there is a metric (easy to evaluate) to
characterize how much the two helix are "around each other" (id est,
how much "coiled-coiled" they are) and, preferably, a software to
calculate this metric.
Thank you,
Jorge
State University of Ponta Grossa
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