Oooh this is a good question. "shape" is one of those concepts that we
think we understand intuitively, but we don't. There's really no single
calculation that describes the shape of a thing as far as I know.
You could measure:
(1) solvent exposed surface area [try eg
http://www.msg.ucsf.edu/local/programs/moloc/surface.html]
(2) inertial tensor.
(3) alpha vs beta conformation of peptides (Ramachandran plot)
(4) concavity of solvent-excluded surface
(5) shape complementarity S_c of individual peptide surfaces (you are
interested in packing them together?)
The fun goes on, sorry for the late answer you have probably come up with
something by now.
Josh
On 4 January 2016 at 12:54, Fabian gmail <fabian.glaser.gmail.com> wrote:
> Hi,
>
> What is the best way to calculate the change in SHAPE of a protein (in my
> specific case an array of peptides) during simulation?
> RMSD helps and also Rg but they don’t give me exactly the change in shape….
>
> Is there a way to do that effectively in cpptraj?
>
> I saw something similar in MDanalysis, but I wouldn’t like to start
> dealing with python issues….
>
> Best and and thanks in advance,
>
> Fabian
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 13 2016 - 03:00:03 PST
