Hi,
The relax paper has been submitted but hasn't been accepted yet. It
is one of a series of four papers submitted together which discuss the
different optimisation aspects within relax. Labelling them Papers I,
II, III, and IV, the one presenting relax is Paper IV. Models m0 to
m9 are presented in Paper I (models m10 to m39 haven't been
discussed). Models tm0 to tm9 are presented in Paper III.
Essentially Paper I presents and compares the optimisation algorithms
used in relax, and compares them with Dasha and Modelfree4. Paper II
is a bit of a review of the model-free field with a twist - it recasts
the entire problem using set theory and presents the universal set and
universal solution (these new concepts are key to the new model-free
protocol presented in Paper III). Paper III re-derives the Brownian
rotational diffusion equations and significantly simplifies them from
an optimisation perspective, presents equations for collapsing the
symmetries of the diffusion parameter space, and presents the new
model-free optimisation protocol coded into the 'full_analysis.py'
script. Paper IV presents relax by reanalysing a recent model-free
publication.
In summary for relax: Paper I = the optimisation algorithms of the
program; Paper II + III = the new model-free protocol in
'full_analysis.py'; Paper IV = relax. The titles are:
Optimisation of NMR dynamic models I. Minimisation algorithms and
their performance within the model-free space.
Optimisation of NMR dynamic models II. Set theory formulation of the
model-free problem and Kay's model-free paradigm.
Optimisation of NMR dynamic models III. Derivation of the Brownian
diffusion correlation functions and a new methodology for the dual
optimisation of the model-free parameters and the diffusion tensor.
Optimisation of NMR dynamic models IV. A new software program for the
study of protein dynamics through NMR relaxation data analysis -
relax.
How you cite the ones you wish to cite would probably depend on your
journal style/convention (for example you may need the journal which
these were submitted to). The authors on all four would be
"d'Auvergne, E. J. and Gooley, P. R.". Between the submission and the
proofing stages of your publication hopefully this series will
progress to 'accepted', 'in press', or published. I could privately
send a draft copy of any of these if you wish.
In addition to these four papers the AIC (or BIC, cross validation,
bootstrap, etc.) model selection and the important 'eliminate()' user
function are discussed in:
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.
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.
Cheers,
Edward
On 11/6/06, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi Edward-
Do you have a paper on relax in the pipeline to be published soon?
Also, do you have any references to other papers discussing the list
of models found in:
Chapter 10 -- ALPHABETICAL LISTING OF USER FUNCTIONS
10.2.29 model free.select model
(m0-m39, tm0-tm39)
Thanks,
Doug
Re: publication(s)