Author: bugman
Date: Tue Feb 16 15:36:32 2010
New Revision: 10707
URL: http://svn.gna.org/viewcvs/relax?rev=10707&view=rev
Log:
Updated the references page to be more relax specific.
This matches the HTML window of references in the Bieri relax GUI.
Modified:
website/refs.html
Modified: website/refs.html
URL:
http://svn.gna.org/viewcvs/relax/website/refs.html?rev=10707&r1=10706&r2=10707&view=diff
==============================================================================
--- website/refs.html (original)
+++ website/refs.html Tue Feb 16 15:36:32 2010
@@ -63,37 +63,72 @@
<div class="main">
<div class="main_box">
<h1>References</h1>
- <ul class="ref_ul">
- <li class="ref_li" id="Chen04"> 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. <em>J. Biomol. NMR</em>, <strong>29</strong>(3), 243-257.</li>
+ <h2>The program relax</h2>
+ <ul class="ref_ul">
+ <li class="ref_li" id="dAuvergneGooley08a">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. <em>J. Biomol. NMR</em>, <strong>40</strong>(2),
107-119. (<a
href="http://dx.doi.org/10.1007/s10858-007-9214-2";>abstract</a>)</li>
- <li class="ref_li" id="Clore90">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. <em>J. Am. Chem. Soc.</em>,
<strong>112</strong>(12), 4989â4991.</li>
+ <li class="ref_li" id="dAuvergneGooley08b">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. <em>J. Biomol. NMR</em>,
<strong>40</strong>(2), 121-133. (<a
href="http://dx.doi.org/10.1007/s10858-007-9213-3";>abstract</a>)</li>
+ </ul>
- <li class="ref_li" id="dAuvergne06">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. (<a
href="http://eprints.infodiv.unimelb.edu.au/archive/00002799/";>abstract</a>,
<a
href="http://eprints.infodiv.unimelb.edu.au/archive/00002799/01/thesis.pdf";>PDF</a>)</li>
- <li class="ref_li" id="dAuvergneGooley03">d'Auvergne, E. J. and Gooley,
P. R. (2003). The use of model selection in the model-free analysis of
protein dynamics. <em>J. Biomol. NMR</em>, <strong>25</strong>(1), 25â39.
(<a href="http://dx.doi.org/10.1023/A:1021902006114";>abstract</a>)</li>
+ <h2>Model-free analysis in relax</h2>
- <li class="ref_li" id="dAuvergneGooley06">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. <em>J. Biomol. NMR</em>,
<strong>35</strong>(2), 117â135. (<a
href="http://dx.doi.org/10.1007/s10858-006-9007-z";>abstract</a>)</li>
+ <p>For a model-free analysis using relax, all of the following should be
cited!</p>
- <li class="ref_li" id="dAuvergneGooley07">d'Auvergne E. J., Gooley P. R.
(2007). Set theory formulation of the model-free problem and the diffusion
seeded model-free paradigm. <em>Mol. Biosyst.</em>, <strong>3</strong>(7),
483-494. (<a href="http://dx.doi.org/10.1039/b702202f";>abstract</a>)</li>
+ <h3>Original Lipari-Szabo theory</h3>
+ <ul class="ref_ul">
+ <li class="ref_li" id="LipariSzabo82a">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. <em>J. Am. Chem. Soc.</em>, <strong>104</strong>(17),
4546â4559.</li>
- <li class="ref_li" id="dAuvergneGooley08a">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. <em>J. Biomol. NMR</em>, <strong>40</strong>(2), 107-119. (<a
href="http://dx.doi.org/10.1007/s10858-007-9214-2";>abstract</a>)</li>
+ <li class="ref_li" id="LipariSzabo82b">Lipari, G. and Szabo, A.
(1982b). Model-free approach to the interpretation of nuclear
magnetic-resonance relaxation in macromolecules II. Analysis of experimental
results. <em>J. Am. Chem. Soc.</em>, <strong>104</strong>(17),
4559â4570.</li>
+ </ul>
- <li class="ref_li" id="dAuvergneGooley08b">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. <em>J. Biomol. NMR</em>, <strong>40</strong>(2),
121-133. (<a
href="http://dx.doi.org/10.1007/s10858-007-9213-3";>abstract</a>)</li>
+ <h3>Extended model-free theory</h3>
+ <ul class="ref_ul">
+ <li class="ref_li" id="Clore90">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. <em>J. Am. Chem. Soc.</em>,
<strong>112</strong>(12), 4989â4991.</li>
+ </ul>
- <li class="ref_li" id="Farrow95">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.
<em>Biochem.</em>, <strong>34</strong>(3), 868-878.</li>
+ <h3>Model-free model selection</h3>
+ <ul class="ref_ul">
+ <li class="ref_li" id="dAuvergneGooley03">d'Auvergne, E. J. and Gooley,
P. R. (2003). The use of model selection in the model-free analysis of
protein dynamics. <em>J. Biomol. NMR</em>, <strong>25</strong>(1), 25â39.
(<a href="http://dx.doi.org/10.1023/A:1021902006114";>abstract</a>)</li>
+ </ul>
- <li class="ref_li" id="Horne07">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 <em>Vibrio
cholerae</em> - a <sup>15</sup>N-<sup>1</sup>H heteronuclear NMR relaxation
analysis of oxidized and reduced forms of DsbA. <em>J. Mol. Biol.</em>,
<strong>371</strong>(3), 703-716. (<a
href="http://dx.doi.org/10.1016/j.jmb.2007.05.067";>abstract</a>)</li>
+ <h3>Model-free model elimination</h3>
+ <ul class="ref_ul">
+ <li class="ref_li" id="dAuvergneGooley06">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. <em>J. Biomol. NMR</em>,
<strong>35</strong>(2), 117â135. (<a
href="http://dx.doi.org/10.1007/s10858-006-9007-z";>abstract</a>)</li>
+ </ul>
- <li class="ref_li" id="Lefevre96">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. <em>Biochem.</em>, <strong>35</strong>(8),
2674â2686.</li>
+ <h3>Model-free minimisation</h3>
+ <ul class="ref_ul">
+ <li class="ref_li">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.
<em>J. Biomol. NMR</em>, <strong>40</strong>(2), 107-119. (<a
href="http://dx.doi.org/10.1007/s10858-007-9214-2";>abstract</a>)</li>
+ </ul>
- <li class="ref_li" id="LipariSzabo82a">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. <em>J. Am.
Chem. Soc.</em>, <strong>104</strong>(17), 4546â4559.</li>
+ <h3>The new model-free analysis protocol</h3>
+ <ul class="ref_ul">
+ <li class="ref_li" id="dAuvergneGooley07">d'Auvergne E. J., Gooley P.
R. (2007). Set theory formulation of the model-free problem and the
diffusion seeded model-free paradigm. <em>Mol. Biosyst.</em>,
<strong>3</strong>(7), 483-494. (<a
href="http://dx.doi.org/10.1039/b702202f";>abstract</a>)</li>
- <li class="ref_li" id="LipariSzabo82b">Lipari, G. and Szabo, A. (1982b).
Model-free approach to the interpretation of nuclear magnetic-resonance
relaxation in macromolecules II. Analysis of experimental results. <em>J. Am.
Chem. Soc.</em>, <strong>104</strong>(17), 4559â4570.</li>
+ <li class="ref_li">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. <em>J. Biomol. NMR</em>, <strong>40</strong>(2), 121-133.
(<a href="http://dx.doi.org/10.1007/s10858-007-9213-3";>abstract</a>)</li>
+ </ul>
- <li class="ref_li" id="Mandel95">Mandel, A. M., Akke, M., and Palmer,
3rd, A. G. (1995). Backbone dynamics of <em>Escherichia coli</em>
ribonuclease HI: correlations with structure and function in an active
enzyme. <em>J. Mol. Biol.</em>, <strong>246</strong>(1), 144â163.</li>
+ <h3>Comprehensive reference</h3>
+ <p>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.</p>
+ <ul class="ref_ul">
+ <li class="ref_li" id="dAuvergne06">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. (<a
href="http://eprints.infodiv.unimelb.edu.au/archive/00002799/";>abstract</a>,
<a
href="http://eprints.infodiv.unimelb.edu.au/archive/00002799/01/thesis.pdf";>PDF</a>)</li>
+ </ul>
- <li class="ref_li" id="Tugarinov01">Tugarinov, V., Liang, Z., Shapiro,
Y. E., Freed, J. H., and Meirovitch, E. (2001). A structural mode-coupling
approach to <sup>15</sup>N NMR relaxation in proteins. <em>J. Am. Chem.
Soc.</em>, <strong>123</strong>(13), 3055â3063.</li>
- </ul>
+ <h2>Misc.</h2>
+ <ul class="ref_ul">
+ <li class="ref_li" id="Chen04"> 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. <em>J. Biomol. NMR</em>, <strong>29</strong>(3), 243-257.</li>
+
+ <li class="ref_li" id="Farrow95">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.
<em>Biochem.</em>, <strong>34</strong>(3), 868-878.</li>
+
+ <li class="ref_li" id="Horne07">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 <em>Vibrio
cholerae</em> - a <sup>15</sup>N-<sup>1</sup>H heteronuclear NMR relaxation
analysis of oxidized and reduced forms of DsbA. <em>J. Mol. Biol.</em>,
<strong>371</strong>(3), 703-716. (<a
href="http://dx.doi.org/10.1016/j.jmb.2007.05.067";>abstract</a>)</li>
+
+ <li class="ref_li" id="Lefevre96">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. <em>Biochem.</em>, <strong>35</strong>(8),
2674â2686.</li>
+
+ <li class="ref_li" id="Mandel95">Mandel, A. M., Akke, M., and Palmer,
3rd, A. G. (1995). Backbone dynamics of <em>Escherichia coli</em>
ribonuclease HI: correlations with structure and function in an active
enzyme. <em>J. Mol. Biol.</em>, <strong>246</strong>(1), 144â163.</li>
+
+ <li class="ref_li" id="Tugarinov01">Tugarinov, V., Liang, Z., Shapiro,
Y. E., Freed, J. H., and Meirovitch, E. (2001). A structural mode-coupling
approach to <sup>15</sup>N NMR relaxation in proteins. <em>J. Am. Chem.
Soc.</em>, <strong>123</strong>(13), 3055â3063.</li>
+ </ul>
</div>
</div>
r10707 - /website/refs.html