References

The following is a list of all references for the software relax.

Harvard style references

The main references for the program relax are [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. The relax GUI reference is [Bieri et al., 2011].

The model-free theory references are [Lipari and Szabo, 1982a][Lipari and Szabo, 1982b][Clore et al., 1990]. Advancements and improvements in the model-free analysis of relaxation data have been performed in [d'Auvergne and Gooley, 2003][d'Auvergne and Gooley, 2006][d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008a][d'Auvergne and Gooley, 2008b][d'Auvergne, 2006]. Consistency testing in relax references are [Morin and Gagné, 2009][Fushman et al., 1999]. N-state model analysis references are [Sun et al., 2011][Erdelyi et al., 2011]. And the relaxation dispersion reference is [Morin et al., 2014].

Full references

The program relax

• [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and 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. (DOI: 10.1039/b702202f)

• [*d'Auvergne and Gooley, 2008b] 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. (DOI: 10.1007/s10858-007-9213-3)

relax GUI

• [*Bieri et al., 2011] Bieri, M., d'Auvergne, E., and Gooley, P. (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, 147-155. (DOI: 10.1007/s10858-011-9509-1)

Model-free analysis in relax

Original Lipari-Szabo theory

• [*Lipari and Szabo, 1982a] Lipari, G. and Szabo, A. (1982). 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. (DOI: 10.1021/ja00381a009)
• [*Lipari and Szabo, 1982b] Lipari, G. and Szabo, A. (1982). 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. (DOI: 10.1021/ja00381a010)

Extended model-free theory

• [*Clore et al., 1990] Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., and Gronenborn, A. M. (1990). 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. (DOI: 10.1021/ja00168a070)

Model-free model selection

• [*d'Auvergne and Gooley, 2003] 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. (DOI: 10.1023/a:1021902006114)

Model-free model elimination

• [*d'Auvergne and Gooley, 2006] 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. (DOI: 10.1007/s10858-006-9007-z)

Model-free minimisation

• [*d'Auvergne and Gooley, 2008a] 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. (DOI: 10.1007/s10858-007-9214-2)

The new model-free analysis protocol

• [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and 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. (DOI: 10.1039/b702202f)
• [*d'Auvergne and Gooley, 2008b] 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. (DOI: 10.1007/s10858-007-9213-3)

Comprehensive reference

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

Consistency testing in relax

• [*Morin and Gagné, 2009] Morin, S. and Gagné, S. (2009). Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45, 361-372. (DOI: 10.1007/s10858-009-9381-4)
• [*Fushman et al., 1999] 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. (DOI: 10.1021/ja9904991)

The N-state model analyses

• [*Sun et al., 2011] 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. Chem. Eur. J., 17(6), 1811-1817. (DOI: 10.1002/chem.201002520)
• [*Erdelyi et al., 2011] Erdélyi, M., d'Auvergne, E., Navarro-Vázquez, A., Leonov, A., and Griesinger, C. (2011). Dynamics of the glycosidic bond: conformational space of lactose. Chem. Eur. J., 17(34), 9368-9376. (DOI: 10.1002/chem.201100854)

The relaxation dispersion analyses

• [*Morin et al., 2014] 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, 30(15), 2219-2220. (DOI: 10.1093/bioinformatics/btu166)

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