· Delarue web servers
· Nomad Flow-chart
· Normal Mode calculation
  · Examples (Movies)
  · Submit a job (from PDB file)
  · Elastic Energy (Perturb. Anal.)
· Overlap coefficients
  · Include Profit step
· Molecular Replacement
  · Split trajectory (for MR)
  · Generate decoys (MixMod)
· X-Ray refinement
  · Standard refinement
  · Screening Mol. Repl. Solns.
· EM refinement
  · Documents/Examples
  · Get Structure Factors
  · Submit a job (no NCS)
  · Submit job with NCS
· Docking refinement
  · Submit a job (refinement)
  · Submit a job (scanning)
· Force field methods
  · Energy minimization
  · Gromacs NMA
· References
· Homes/Links
· Job queue status

If you find this site useful, please cite this Reference.

This site provides tools for online normal mode calculation, even for large proteins and including all atoms, and algorithms that use normal modes for structural refinement or optimization.
Throughout this web site, we mostly use the so-called Elastic Network Model (ENM), originally due to M. Tirion (1996), to calculate Normal Modes, although we do provide an option to calculate them with classical force fields.

Here, we are not only concerned with the calculation of Normal Modes, for which there exists a number of other web sites (although we do provide tools to generate and use them), but we focus more specifically in using Normal Modes as a basis set of collective movements for macromolecules, that are then used to:

  • generate alternative models with correct stereochemistry but large amplitude movements
  • refine models against experimental data such as X-Ray diffraction or cryo-EM data
  • refine docking solutions in cases where it is known that the receptor is flexible
  • Pick a choice in the menu to the left and play around with it - things are still in development.

    The usefuless of this approach to study the interconversion of a macromolecule between two forms has been by and large demonstrated by Tama and Sanejouand (2001), Krebs et al. (2002) and Delarue and Sanejouand (2002) (References). One crucial point is to project eigenvectors of the first low-frequency 100 normal modes onto the difference vectors set between the two forms. One then often sees very large overlaps (>0.7) for a handful of modes (see Figure below).

    This plot represents the overlap coefficient for the first 106 lowest frequency modes of the two forms (open and closed) of maltodextrin binding protein (1ANF and 1OMP). The set of difference vectors between the two forms is projected, in turn, onto the set of each normal mode eigenvectors.
    The green curve corresponds to the case where the Normal Modes are calculated from the open form, the red curve when they are calculated from the closed form.

      Marc Delarue http://lorentz.dynstr.pasteur.fr
    Page last modified 16:23 September 20, 2006.