[MMTK] ENM normal mode analysis question

Konrad Hinsen research at khinsen.fastmail.net
Sat Jun 1 07:10:23 UTC 2013

Liz Kellogg writes:

 > I'm new to the group, and I've been searching all over google to see if 
 > what i want to do is possible in MMTK. Perhaps someone here can answer.
 > I have 3 different protein structures, and I want to perform normal mode 
 > analysis on the C-alphas (I think I need to use the elastic network 
 > model) to try and resolve the structural changes going from one 
 > conformation to the other. How do I go about doing this in MMTK?
 > Do I read in the pdbs as a trajectory and create a universe from that, 
 > then perform normal mode analysis on the universe?

This is definitely doable with MMTK, but if you want more precise
guidance, we need more details about you want to do. In particular,
are you considering three different structures for the same protein,
or three different but somehow related proteins? And what exactly
do you mean by "resolving" the structural changes?

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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