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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.
One novelty, compared to other web-sites-based methods based on Elastic Networks, is the use of
Delaunay tessalation to define linked neighbours in the Network Model (1), instead of relying on a rather arbitrary radial cutoff.
Also, 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).
Another 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 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).
-One trivial way is to select atoms (beads) based on their names in each amino-acid.
Indeed we provide services that allows to select a few representative points per amino-acid (2), or nucleotide (3-5).
-A more rigourous "projection" of the Hessian of an all-atoms elastic model onto a CA-only network whose force constants are re-calculated has been implemented. It proceeds along lines
described by Na and Song (6) and others.
-Additionnally, we implemented a method that "prunes" the Network beyond the CA-only bead model by the so-called Decimation method
(see Illustration here), using a rigourous algorithm designed to keep the low-frequency modes of the model
(Koehl et al., 2017).
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:
1. Patrice Koehl's method and code for NMA and Delaunay.
2. 2-3 beads per amino-acid: simplified representation of proteins.
3. 6-7 beads per nucleotide: simplified representation of nucleic acids.
4. Elastic Models and RNA structures.
5. Comparison of Elastic Models for RNA with MD and experiments.
6. Rigourous projection method onto CA-only model.
7. Improved Elastic Network with a Go-like Energy.
8. Universality of vibrational spectra of Proteins.
This is a Beta version web site - still under development....