· 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

References

General elastic network theory

Applications to structural transitions

X-ray refinement

Refinement into cryo-EM maps

  • Hinsen K., Reuter N., Navaza J., Stokes D.L. and Lacapere J.J.
    Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase.
    Biophys. J., 88:818-827 (2005).
  • Tama F., Miyashita O. and Brooks C.L. III
    Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.
    J. Mol. Biol., 337:985-99 (2004).

Docking refinement

Web site

  • Lindahl, E., Azuara, C., Koehl, P. and Delarue, Marc.
    NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom Normal Mode Analysis.
    Nucleic Acids Res. (2006) 34: W52-56. On-line article

Review

  • Delarue, Marc.
    Dealing with structural variability in molecular replacement and crystallographic refinement through Normal Mode Analysis.
    Acta Cryst. (2008) D64: 40-48. Summary

Recent

  • Schroder, G.F., Brunger, A.T. and Levitt, M.
    Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.
    Structure (2007) 15: 1630-41. Link



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:02 January 24, 2006.