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· Protein CG
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· Decimation CG
· New NMA Models
· Go-like Energy NMA
· Delaunay + classic NMA
· Job queue status
· Distances Bridges
Welcome to DD-NMA website (beta-version)
This site provides tools for calculating Normal Modes using either Full-atomic or Coarse-Grained Models of Proteins and Nucleic Acids using a variant of the Elastic Network, with no adjustable parameter.
It allows to calculate Normal Modes for very large macromolecular assemblies as large as complete
viral capsids (Koehl and Delarue, 2019).
It is the collaborative work of Fred Poitevin, Rafael Navaza, Marc Delarue and Patrice Koehl.
On one hand it permits to define the Network based on Delauney representation of proteins,
and it does not rely on any cutoff to define the neighbours of each node (Ref 1).
On the other hand, it allows several ways to coarse-grain the molecule, from the simplest method
(Refs 2-3) to the more sophisticated and rigourous Decimation method, described
The code for Normal Modes calculation itself has been rewritten to accommodate very large structures, comprising up to than 300,000 atoms.
One novelty is a more systematic way to achieve coarse-graining.
Finally, the last major novelty is the implementation of the calculation of Normal Modes using a Hessian derived from a more complete Go-like energy, that
includes not only a term on distances, but also three additional elastic terms based on three-body and four-body (dihedral) angles (7).
In this way, we depart from the classical Elastic Network defined originally by Monique Tirion, while keeping most of its salient features (8).
Key References can be found here:
This is a Beta version web site - still under development....
Page last modified 21:14 October 29, 2020.