Literature DB >> 23456039

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

Jonathan J Helmus1, Christopher P Jaroniec.   

Abstract

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

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Year:  2013        PMID: 23456039      PMCID: PMC3636164          DOI: 10.1007/s10858-013-9718-x

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  32 in total

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Authors:  Wyndham B Blanton
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2.  Rapid acquisition of multidimensional solid-state NMR spectra of proteins facilitated by covalently bound paramagnetic tags.

Authors:  Philippe S Nadaud; Jonathan J Helmus; Ishita Sengupta; Christopher P Jaroniec
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3.  Molecular conformation and dynamics of the Y145Stop variant of human prion protein in amyloid fibrils.

Authors:  Jonathan J Helmus; Krystyna Surewicz; Philippe S Nadaud; Witold K Surewicz; Christopher P Jaroniec
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4.  Transverse-dephasing optimized homonuclear j-decoupling in solid-state NMR spectroscopy of uniformly 13C-labeled proteins.

Authors:  Ségolène Laage; Anne Lesage; Lyndon Emsley; Ivano Bertini; Isabella C Felli; Roberta Pierattelli; Guido Pintacuda
Journal:  J Am Chem Soc       Date:  2009-08-12       Impact factor: 15.419

5.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

6.  Evaluation of the influence of intermolecular electron-nucleus couplings and intrinsic metal binding sites on the measurement of 15N longitudinal paramagnetic relaxation enhancements in proteins by solid-state NMR.

Authors:  Philippe S Nadaud; Ishita Sengupta; Jonathan J Helmus; Christopher P Jaroniec
Journal:  J Biomol NMR       Date:  2011-08-09       Impact factor: 2.835

7.  A covariance NMR toolbox for MATLAB and OCTAVE.

Authors:  Timothy Short; Leigh Alzapiedi; Rafael Brüschweiler; David Snyder
Journal:  J Magn Reson       Date:  2010-12-05       Impact factor: 2.229

8.  Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

Authors:  Krzysztof Gorgolewski; Christopher D Burns; Cindee Madison; Dav Clark; Yaroslav O Halchenko; Michael L Waskom; Satrajit S Ghosh
Journal:  Front Neuroinform       Date:  2011-08-22       Impact factor: 4.081

9.  Paramagnetic ions enable tuning of nuclear relaxation rates and provide long-range structural restraints in solid-state NMR of proteins.

Authors:  Philippe S Nadaud; Jonathan J Helmus; Stefanie L Kall; Christopher P Jaroniec
Journal:  J Am Chem Soc       Date:  2009-06-17       Impact factor: 15.419

10.  Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy.

Authors:  Ishita Sengupta; Philippe S Nadaud; Jonathan J Helmus; Charles D Schwieters; Christopher P Jaroniec
Journal:  Nat Chem       Date:  2012-03-18       Impact factor: 24.427

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  81 in total

1.  Non-uniform sampling of NMR relaxation data.

Authors:  Troels E Linnet; Kaare Teilum
Journal:  J Biomol NMR       Date:  2016-02-04       Impact factor: 2.835

2.  Speeding-up exchange-mediated saturation transfer experiments by Fourier transform.

Authors:  Marta G Carneiro; Jithender G Reddy; Christian Griesinger; Donghan Lee
Journal:  J Biomol NMR       Date:  2015-09-09       Impact factor: 2.835

3.  Conformational Dynamics of the HIV-Vif Protein Complex.

Authors:  K Aurelia Ball; Lieza M Chan; David J Stanley; Elise Tierney; Sampriti Thapa; Hai M Ta; Lily Burton; Jennifer M Binning; Matthew P Jacobson; John D Gross
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4.  Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR.

Authors:  Dwaipayan Mukhopadhyay; Chitrak Gupta; Theint Theint; Christopher P Jaroniec
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Review 5.  Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy.

Authors:  Leonid S Brown; Vladimir Ladizhansky
Journal:  Protein Sci       Date:  2015-05-27       Impact factor: 6.725

6.  Protein structural studies by paramagnetic solid-state NMR spectroscopy aided by a compact cyclen-type Cu(II) binding tag.

Authors:  Ishita Sengupta; Min Gao; Rajith J Arachchige; Philippe S Nadaud; Timothy F Cunningham; Sunil Saxena; Charles D Schwieters; Christopher P Jaroniec
Journal:  J Biomol NMR       Date:  2014-11-29       Impact factor: 2.835

7.  Detection of chemical exchange in methyl groups of macromolecules.

Authors:  Michelle L Gill; Andrew Hsu; Arthur G Palmer
Journal:  J Biomol NMR       Date:  2019-08-12       Impact factor: 2.835

8.  Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND.

Authors:  Jia Xu; Steven R Van Doren
Journal:  Biophys J       Date:  2017-01-24       Impact factor: 4.033

9.  Practical considerations for investigation of protein conformational dynamics by 15N R relaxation dispersion.

Authors:  Erik Walinda; Daichi Morimoto; Masahiro Shirakawa; Kenji Sugase
Journal:  J Biomol NMR       Date:  2017-02-28       Impact factor: 2.835

10.  Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.

Authors:  Matthew D Shannon; Theint Theint; Dwaipayan Mukhopadhyay; Krystyna Surewicz; Witold K Surewicz; Dominique Marion; Paul Schanda; Christopher P Jaroniec
Journal:  Chemphyschem       Date:  2018-11-07       Impact factor: 3.102

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