Author: bugman
Date: Tue Nov 13 14:32:45 2012
New Revision: 17955
URL: http://svn.gna.org/viewcvs/relax?rev=17955&view=rev
Log:
Added a temporary page for the MARC archives.
This includes the links:
http://marc.info/?l=relax-announce
http://marc.info/?l=relax-users
http://marc.info/?l=relax-devel
http://marc.info/?l=relax-commits
Added:
website/marc.html
- copied, changed from r17939, website/refs.html
Copied: website/marc.html (from r17939, website/refs.html)
URL:
http://svn.gna.org/viewcvs/relax/website/marc.html?p2=website/marc.html&p1=website/refs.html&r1=17939&r2=17955&rev=17955&view=diff
==============================================================================
--- website/refs.html (original)
+++ website/marc.html Tue Nov 13 14:32:45 2012
@@ -21,103 +21,15 @@
<body>
<!--#include virtual="header.html" -->
-<!--#include virtual="menu.html" -->
<div class="main">
<div class="main_box">
- <h1>References</h1>
+ <h1>MARC (Mailing list ARChives) links</h1>
- <div class="main_h2" id="relax">
- <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="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>
-
- <h3>relax GUI</h3>
- <ul class="ref_ul">
- <li class="ref_li" id="Bieri11">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. <em>J.
Biomol. NMR</em>, <strong>50</strong>(2), 147-155. (<a
href="http://dx.doi.org/10.1007/s10858-011-9509-1";>abstract</a>)</li>
- </ul>
- </div>
-
-
- <div class="main_h2" id="model_free">
- <h2>Model-free analysis in relax</h2>
-
- <p>For a model-free analysis using relax, all of the following should be
cited!</p>
-
- <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), 4546-4559.
(<a href="http://dx.doi.org/10.1021/ja00381a009";>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), 4559-4570.
(<a href="http://dx.doi.org/10.1021/ja00381a010";>abstract</a>)</li>
- </ul>
-
- <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), 4989-4991. (<a
href="http://dx.doi.org/10.1021/ja00168a070";>abstract</a>)</li>
- </ul>
-
- <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), 25-39. (<a
href="http://dx.doi.org/10.1023/A:1021902006114";>abstract</a>)</li>
- </ul>
-
- <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), 117-135. (<a
href="http://dx.doi.org/10.1007/s10858-006-9007-z";>abstract</a>)</li>
- </ul>
-
- <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>
-
- <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">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>
-
- <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>
- </div>
-
- <div class="main_h2" id="consistency_testing">
- <h2>Consistency testing in relax</h2>
- <ul class="ref_ul">
- <li class="ref_li" id="Morin09">Morin, S. and Gagné, S. M.
(2009). Simple tests for the validation of multiple field spin relaxation
data. <em>J. Biomol. NMR</em>, <strong>45</strong>(4), 361-372. (<a
href="http://dx.doi.org/10.1007/s10858-009-9381-4";>abstract</a>)</li>
- <li class="ref_li" id="Fushman99">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. <em>J. Am.
Chem. Soc.</em>, <strong>121</strong>(37), 8577-8582. (<a
href="http://dx.doi.org/10.1021/ja9904991";>abstract</a>)</li>
- </ul>
- </div>
-
- <div class="main_h2" id="n_state">
- <h2>The N-state model analyses</h2>
- <ul class="ref_ul">
- <li class="ref_li" id="Sun11">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. <em>Chemistry-A European Journal</em>, <strong>17</strong>(6),
1811-1817. (<a
href="http://dx.doi.org/10.1002/chem.201002520";>abstract</a>)</li>
- <li class="ref_li" id="Erdelyi11">Erdelyi, M., d'Auvergne, E.,
Navarro-Vazquez, A., Leonov, A., and Griesinger, C. (2011). Dynamics of the
Glycosidic Bond: Conformational Space of Lactose. <em>Chemistry-A European
Journal</em>, <strong>17</strong>(34), 9368-9376. (<a
href="http://dx.doi.org/10.1002/chem.201100854";>abstract</a>)</li>
- </ul>
- </div>
-
- <div class="main_h2" id="misc">
- <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. (<a
href="http://dx.doi.org/10.1023/b:jnmr.0000032504.70912.58";>abstract</a>)</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. (<a
href="http://dx.doi.org/10.1021/bi00003a021";>abstract</a>)</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), 2674-2686. (<a
href="http://dx.doi.org/10.1021/bi9526802";>abstract</a>)</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), 144-163. (<a
href="http://dx.doi.org/10.1006/jmbi.1994.0073";>abstract</a>)</li>
- </ul>
- </div>
+ <a href="http://marc.info/?l=relax-announce";>MARC (Mailing list
ARChives) for relax-announce</a>
+ <a href="http://marc.info/?l=relax-users";>MARC (Mailing list
ARChives) for relax-users</a>
+ <a href="http://marc.info/?l=relax-devel";>MARC (Mailing list
ARChives) for relax-devel</a>
+ <a href="http://marc.info/?l=relax-commits";>MARC (Mailing list
ARChives) for relax-commits</a>
</div>
</div>
r17955 - /website/marc.html