relax: dynamics analysis, model-free analysis, relaxation data, R1 and R2 exponential curve-fitting, steady-state NOE calculation, reduced spectral density mapping, relaxation dispersion, N-state model, frame order dynamics theories, stereochemistry, conformational analysis, organic molecules, proteins, RNA, DNA, sugars, and other biomolecules.

relax - Molecular dynamics by NMR data analysis

Analysis software for: Model-free, NMR relaxation (R1, R2, NOE), reduced spectral density mapping, relaxation dispersion, N-state models, frame order theory.

References

The program relax

  • d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119. (abstract)
  • d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (abstract)

relax GUI

  • Bieri M., d'Auvergne E. J., Gooley P. R. (2011). relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins. J. Biomol. NMR, 50(2), 147-155. (abstract)

Model-free analysis in relax

For a model-free analysis using relax, all of the following should be cited!

Original Lipari-Szabo theory

  • Lipari, G. and Szabo, A. (1982a). Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules I. Theory and range of validity. J. Am. Chem. Soc., 104(17), 4546-4559. (abstract)
  • Lipari, G. and Szabo, A. (1982b). Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results. J. Am. Chem. Soc., 104(17), 4559-4570. (abstract)

Extended model-free theory

  • Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., and Gronenborn, A. M. (1990b). Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins. J. Am. Chem. Soc., 112(12), 4989-4991. (abstract)

Model-free model selection

  • d'Auvergne, E. J. and Gooley, P. R. (2003). The use of model selection in the model-free analysis of protein dynamics. J. Biomol. NMR, 25(1), 25-39. (abstract)

Model-free model elimination

  • d'Auvergne, E. J. and Gooley, P. R. (2006). Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR, 35(2), 117-135. (abstract)

Model-free minimisation

  • d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119. (abstract)

The new model-free analysis protocol

  • d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. Biosyst., 3(7), 483-494. (abstract)
  • d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (abstract)

Comprehensive reference

This PhD thesis expands on all of the d'Auvergne and Gooley references and describes model-free analysis and the program relax in more detail.

  • d'Auvergne, E. J. (2006). Protein dynamics: a study of the model-free analysis of NMR relaxation data. Ph.D. thesis, Biochemistry and Molecular Biology, University of Melbourne. (abstract, PDF)

It is also available in published book form.

Consistency testing in relax

  • Morin, S. and Gagné, S. M. (2009). Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45(4), 361-372. (abstract)
  • Fushman, D., Tjandra, N., and Cowburn, D. (1999). An approach to direct determination of protein dynamics from 15N NMR relaxation at multiple fields, independent of variable 15N chemical shift anisotropy and chemical exchange contributions. J. Am. Chem. Soc., 121(37), 8577-8582. (abstract)

The N-state model analyses

  • Sun, H., d'Auvergne, E. J., Reinscheid, U. M., Dias, L. C., Andrade, C. K. Z., Rocha, R. O., and Griesinger, C. (2011). Bijvoet in solution reveals unexpected stereoselectivity in a michael addition. Chemistry-A European Journal, 17(6), 1811-1817. (abstract)
  • Erdelyi, M., d'Auvergne, E., Navarro-Vazquez, A., Leonov, A., and Griesinger, C. (2011). Dynamics of the Glycosidic Bond: Conformational Space of Lactose. Chemistry-A European Journal, 17(34), 9368-9376. (abstract)

The relaxation dispersion analyses

  • Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., Teilum, K., Gagné, S., Marion, D., Griesinger, C., Blackledge, M., and d'Auvergne, E. J. (2014). relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. (abstract)

Misc.

  • Chen, J., Brooks, 3rd, C. L., and Wright, P. E. (2004). Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J. Biomol. NMR, 29(3), 243-257. (abstract)
  • Farrow, N. A., Zhang, O., Forman-Kay, J. D., Kay, L. E. (1995). Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochem., 34(3), 868-878. (abstract)
  • Horne J., d'Auvergne E. J., Coles M., Velkov T., Chin Y., Charman W. N., Prankerd R., Gooley P. R., Scanlon M. J. (2007). Probing the flexibility of the DsbA oxidoreductase from Vibrio cholerae - a 15N-1H heteronuclear NMR relaxation analysis of oxidized and reduced forms of DsbA. J. Mol. Biol., 371(3), 703-716. (abstract)
  • Lefevre, J. F., Dayie, K. T., Peng, J. W., and Wagner, G. (1996). Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. Biochem., 35(8), 2674-2686. (abstract)
  • Mandel, A. M., Akke, M., and Palmer, 3rd, A. G. (1995). Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol., 246(1), 144-163. (abstract)