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Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / Marion Dominique

Non linear Fourier transform of NMR data acquired on a non-cartesian sampling grid

Presentation

In the field of biological NMR, a very active research is carried out in methods requiring less time for acquiring data. Multiple multidimensional NMR spectra that are employed to enable sequence specific assignment and to obtain structural information, typically take days and weeks of instrument time. The introduction of higher field magnets requires more frequent sampling (larger spectral width) and simultaneously an increase in the number of samples (better spectral resolution). In order to reduce the experimental time, several groups have proposed alternatives to standard cartesian sampling (reduced dimensionality experiments...) that can unfortunately not be processed using simple fast Fourier transform (FFT). These new techniques involve also drawbacks such as the occurrence of aliasing artefacts in the frequency domain which can be erroneously interpreted as signals by an unexperienced user or an automated peakpicking program. More recently, random sampling schemes have been introduced which eliminated these systematic artefacts.
Data sampled with non standard schemes can be processed using iterative algorithms (such as maximum entropy reconstruction or three-way decomposition) that require a lot of expertise to yield uncorrupted spectra. We have recently shown that a modified implementation of the Fourier transform (i.e. a non iterative algorithm) can also be used without requiring any tedious optimisation of the processing parameters. A software package to generate the acquisition delays for random sampling and process data (together with the nmrPipe software suite) is described here. The programs have been compiled for the following platforms : Linux and Mac OS (10.4)

Reference:
Pannetier N, Houben K, Blanchard L, Marion D.
J Magn Reson. 2007 186: 142-149
Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins.

Program and copyright

The NonLinearFT program Version 1.0 Jan 2007 Copyright © 2007 CEA/CNRS/UJF. All Rights Reserved. Laboratoire de Résonance Magnetique Nucléaire IBS 2007

The NonLinearFT program is copyrighted and was developed by Nicolas Pannetier and Dominique Marion at the Laboratoire de Résonance Magnétique Nucleaire in the Institut de Biologie Structurale - Jean-Pierre Ebel (CEA - CNRS - UJF) at Grenoble, France.

The license is free for academic sites and non commercial use . The use of the program is subject to the following conditions: The use of the program is restricted to the individual, laboratory or organization to which it is supplied. This individual, laboratory or organization can make unlimited copies of the program for backup purposes or for running the program on more than one computer system at the host institution. Neither the program nor any part of it may be sold, nor any copies distributed to third parties without the express permission of the authors at the Institut de Biologie Structurale. Users may not decompile, disassemble, reverse engineer or modify the program in any way. No software package can be considered to be bug free. The authors of the NonLinearFT program accept no responsability whatsoever for damages resulting, directly or indirectly, from the downloading and the use of the program and make no warranty, either express or implied, including but not limited to, any implied warranty of fitness for particular purpose. The NonLinearFT program is provided as it is and its users shall assume any loss, risk and damage when using it. If any results obtained with the NonLinearFT program are published, whatever the means of publication, particularly in the scientific literature, the program should be referenced in the following way: Pannetier N, Houben K, Blanchard L, Marion D. J Magn Reson. 2007 Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins.

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