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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.
It is the collaborative work of Fred Poitevin, Marc Delarue and Patrice Koehl.
The code for Normal Modes calculation itself has been rewritten to accommodate very large structures, comprising up to than 300,000 atoms.
A recent application handling very large macromolecular complexes such as entire viruses (Frontiers in Molecular Biosciences, 2017).
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 15:42 May 08, 2017.