· Delarue web servers
· Nomad Flow-chart
· Normal Mode calculation
· Examples (Movies)
· Submit a job (from PDB file)
· Elastic Energy (Perturb. Anal.)
· Overlap coefficients
· Include Profit step
· Molecular Replacement
· Split trajectory (for MR)
· Generate decoys (MixMod)
· 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
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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
Applications to structural transitions
X-ray refinement
- 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
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
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