· 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 step
· 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

X-ray refinement

As more and more structures of macromolecular complexes get solved in different conditions, it has become apparent that flexibility is an inherent part of their biological function. Normal mode analysis using simplified models of proteins such as the elastic network model has proved very effective in showing that many of the structural transitions derived from a survey of the Protein Data Bank can be explained by just a few of the lowest-frequency normal modes. See Krebs et al. (2002) and Delarue and Sanejouand (2002) articles in the References section.

This server uses normal modes to perform medium- or low-resolution structural refinement, enforcing collective and large-amplitude movements that are beyond the reach of existing methods. The refinement is carried out in reciprocal space with respect to the normal mode amplitudes, using standard conjugate-gradient optimization. See the Delarue and Dumas (2004) article in the References section.

Choose one of the options in the menu on the left: it can be either standard refinement in any space group, or PC-refinement after the rotation function of the Molecular Replacement (in P1); in the latter case, it needs a list of possible solutions specified by their eulerian angles (alpha, beta, gamma).




  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 11:39 March 01, 2006.