References

General elastic network theory

• Tirion, Monique M.
  Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.
  Phys Rev Lett, 77, 1905--1908 (1996).


• Bahar I, Atilgan AR, Erman, B.
  Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
  Folding and Design, 1, 357-70 (1997).


• Hinsen, Konrad.
  Analysis of domain motions by approximate normal mode calculations.
  Proteins, 33, 417-429 (1998).

Visit Konrad Hinsen web site and on-line tools!

• Tama, Florence & Sanejouand, Yves-Henri.
  Conformational change of proteins arising from normal mode calculations.
  Prot. Eng., 14, 1--6 (2001). Link

• Suhre, Karsten, and Sanejouand, Yves-Henri.
  ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.
  Nucleic Acids Res., 32, W610-614 (2004).

Visit Karsten Suhre web site and on-line tools!

Applications to structural transitions

• Delarue, Marc & Sanejouand, Yves-Henri.
  Simplified Normal Mode Analysis of Conformational Transitions in DNA-dependent Polymerases: the Elastic Network Model.
  J. Mol. Biol., 320, 1011-1024 (2002). PDF
• Krebs W.G., Alexandrov V., Wilson C.A., Echols N., Yu H., Gerstein M.
  Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
  Proteins, 48, 682--695 (2002).
• Franklin J., Koehl P., Doniach S. and Delarue M.
  MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.
  Nucl. Ac. Res., 35, W47--51 (2007).

• Delarue, Marc & Dumas, Phillipe.
  On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models.
  Proc. Natl. Acad. Sci. (USA), 101, 6957-6962 (2004). PDF

• Suhre, Karsten, and Sanejouand, Yves-Henri.
  On the potential of normal mode analysis for solving difficult molecular replacement problems.
  Acta Cryst., D60, 796-799 (2004).

• Claude, J.B., Suhre, K., Notredame, C., Claverie, J.M. and Abergel, C.
  CaspR: a web server for automated molecular replacement using homology modelling.
  Nucleic Acids Res., 32, W606-609 (2004).

Visit Karsten Suhre web site and on-line tools!

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

• Lindahl, Erik & Delarue, Marc.
  Docking Refinement using Low Frequency Normal Mode Amplitude Optimization.
  Nucleic Acids Res. (2005) 33: 4496-4506. On-line article

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