· Delarue web servers
· Nomad Flow-chart
· Normal Mode calculation
  · Examples (Movies)
  · Submit a job (from PDB file)
  · Split trajectory (for MR)
  · Generate decoys (MixMod)
  · Elastic Energy (Perturb. Anal.)
· Overlap coefficients
  · Submit a job
  · Include Profit
· 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
· Force field methods
  · Energy minimization
  · Gromacs NMA
· References
· Homes/Links
· Job queue status

Normal Modes Overlap coefficient calculation

Web Interface of Yves-Henri Sanejouand Program to calculate overlap coefficients between the set of difference vectors of two forms of the same molecule and the eigenvectors of the 100 slowest-frequency modes eigenvectors.
This produces the kind of plot shown below. See Reference list for Tama and Sanejouand (2001) article explaining the meaning of this overlap coefficient here.
You can either (see menu on the left) work with un-superposed or pre-superposed molecules.
For practical purposes, the number of atoms (or residues if CA atoms are used) is limited to about 1000. If you need more, then the RTB method should be used. Please send an e-mail to me and I will assist you (delarue@pasteur.fr).

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 13:07 January 25, 2006.