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Software

You can find below links to download the software developed by the NMR team at ICSN.

- NOENET

- BATCH

- ASCOM

NOEnet (by Dirk Stratmann, Carine van Heijenoort and Eric Guittet)

NOEnet is a program to obtain the NMR resonance assignment of the protein backbone by exploiting an available 3D structure of the protein. Compared to the standard NMR assignment approach which is based on sequential J-coupling connectivities involving 13C, 15N and 1H nuclei, the structure-based assignment approach of NOEnet uses a completely independent data set, based on spatial NOE-connectivities among HN-HN nuclei. The comparison of the NOE-network with the 3D structure yields already satisfactory assignment results, which are improved by the addition of chemical shift (CS) and/or residual dipolar coupling (RDC) data. One step further, the combination of the two orthogonal data sources - J-coupling and NOE - gives very good assignment results, even for large proteins or difficult cases. The structure-based assignment approach of NOEnet is therefore a promising alternative to the standard NMR assignment approach and at the same time a helpful complement to it.

The license is free for academic sites and non commercial use.

Download NOEnet 1.0 for Linux
Download NOEnet 1.0 for Mac-OSX (PowerPC or Intel)
Download NOEnet 1.0 for Windows

Please, send comments or bugs reports to : dirkpascal_at_gmx.de (replace _at_ by the correct symbol)

References :

- Stratmann D, van Heijenoort C, Guittet E. NOEnet—use of NOE networks for NMR resonance assignment of proteins with known 3D structure. Bioinformatics 2009 25(4):474-481

- Stratmann D, Guittet E, van Heijenoort C. Robust structure-based resonance assignment for functional protein studies by NMR. J Biomol NMR 2010 Feb ;46(2):157-73

[3] Documentation of NOEnet :
PDF - 765.3 ko
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BATCH (by Ewen Lescop and Bernhard Brutscher, IBS Grenoble)

BATCH is a strategy to speedup the backbone resonance assignment step of small to medium size proteins (<100aa). It includes several tools contained in its name : BEST/ASCOM/Targeted sampling/COBRA and HADAMAC. BATCH is also the name of the computer program developped to facilitate the data processing, analysis and the final backbone resonance assignment step. It represents a new module in NMRView and provides an interface for NMRPipe.

The license is free for academic sites and non commercial use :

Please, send comments or bugs reports to : Lescop

Download BATCH_v1.3

References :
- Brutscher B, Lescop E. « Fast protein backbone NMR resonance assignment using the BATCH strategy. » Methods Mol Biol. (2012), 831:407-28.
- Lescop E and Brutscher B. « Highly automated protein backbone resonance assignment within a few hours : the "BATCH" strategy and software package. », J Biomol NMR. 2009, 44(1), 43-57.

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ASCOM (by Ewen Lescop and Bernhard Brutscher, IBS Grenoble)

ASCOM is a program developped to automatically optimize spectral width in multidimensional experiments based on the previous knowledge of peak positions. ASCOM Version 2.2 exists as three implementations : (1) X=15N or 13C spectral width optimization of a 1H-X correlation plane, (2) combined 15N and 13C spectral widths optimization in a 3D 1H-15N-13C correlation spectrum ; alternatively, the projection angles and tilted spectral width along the projected 15N /13C dimension, (3) combined 1H-X spectral widths optimization of a 1H-X correlation plane. The program is written in Perl language and works on any operating system.

The license is free for academic sites and non commercial use :

Please, send comments or bugs reports to : Lescop

Download ASCOM_v2.2

Reference : Lescop E, Schanda P, Rasia R, Brutscher B. « Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. » J Am Chem Soc. 2007,14 ;129(10):2756-2757.

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