Follow-up Comment #1, task #6784 (project relax):
The attached PDF file is my 2009 ENC poster. The title is "A toolkit for
dynamics and how to relax the BMRB". The abstract, which is a little
different from the poster, is:
How to relax the BMRB
Edward d'Auvergne
Max-Planck Institute for Biophysical Chemistry, NMR-based Structural Biology,
Am Fassberg 11, 37077 Göttingen, Germany
The program relax [1, 2] (http://nmr-relax.com) is designed for the analysis
of molecular dynamics using experimental NMR data. Currently relax’s
primary purpose is to perform the Lipari-Szabo model-free analysis of
relaxation data. Additionally relax can perform reduced spectral density
mapping [3, 4], exponential curve-fitting for determining R1 and R2
relaxation rates from peak intensities, and calculation of the steady-state
NOE. It provides a set of modular tools for performing highly accurate and
high quality analyses including Monte Carlo simulations, the gold standard
for error propagation and analysis, many high-precision optimisation
algorithms, a selection of techniques from the advanced statistical field of
mathematical model selection (using Frequentist rather than Baysian methods),
and model elimination for the removal of failed models. relax can interface
with other programs including Molmol, PyMOL, Grace, and OpenDX for data
visualisation, and both Dasha and Art Palmer’s Modelfree. For the later
two, relax can create input files, execute in-line, and read the output
results files, effectively allowing relax to use both Dasha and Modelfree as
replacement optimisation engines. Its Python prompt and script interfaces
allow for very powerful and automatic scripting, such as the provided
‘full_analysis.py’ script which performs the new model-free analysis
protocol as descibed in [2]. More details about the full set of features can
be found at [5].
Open source licensing and the flexible, modular architecture allows others to
extend relax to their needs. For instance a number of relax branches are
under current development by various NMR spectroscopists to allow relax to
run on large clusters using the MPI protocol, to perform relaxation
dispersion analyses, to handle ellipsoidal CS tensors for RNA and DNA
analysis, to name a few.
Although hundreds of model-free analyses have been published to date,
providing a wealth of information covering macromolecular motions over the
pico- to nanosecond timescales, most of this data is not easily available, or
even inaccessible to current researchers preventing downstream usage. The
BioMagResBank (BMRB, http://www.bmrb.wisc.edu/) provides the resources to
store all of this data, yet these facilities are rarely used. To improve the
utility of NMR dynamics data, relax is being designed to produce full BMRB
NMR-STAR v3.1 formatted files to facilitate data submission. Once a
model-free analysis has been performed, the BMRB input file can be generated
very easily and submitted prior to manuscript publication.
[imagine a picture of a butterfly]
Figure 1. This is the relax logo. It has absolutely nothing to do with
anything.
[1] 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.
[2] 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.
[3] Farrow, N. A., Zhang, O., Forman-Kay, J. D., Kay, L. E. (1995). Biochem.,
34(3), 868-878.
[4] Lefevre, J. F., Dayie, K. T., Peng, J. W., and Wagner, G. (1996).
Biochem., 35(8), 2674-2686.
[5] 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. (Available in paperback form from
amazon.com).
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[task #6784] relax posters.