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  · Introduction
· Coarse-Graining
  · Protein CG
  · DNA/RNA CG
· Non-constant Kij
  · Hessian Proj. CG
  · Decimation CG
· New NMA Models
  · Go-like Energy NMA
  · Delaunay + classic NMA
· References
· Links
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· Distances Bridges

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 11:22 December 30, 2015.