Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machineÂ*archival and retrieval of the â??missingâ?? metadata.
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction
Abstract
CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy...
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06-12-2015 07:07 AM
[NMR paper] Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
J Biomol NMR. 2014 Jun;59(2):57-73
Authors: Suiter CL, Paramasivam S, Hou G, Sun S, Rice D, Hoch JC, Rovnyak D, Polenova T
...
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12-31-2014 06:44 PM
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range
Abstract
Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high...
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06-19-2014 10:21 PM
CONNJUR spectrum translator: an open source application for reformatting NMR spectral data
CONNJUR spectrum translator: an open source application for reformatting NMR spectral data
Abstract NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two...
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03-18-2011 06:51 PM
A novel strategy for NMR resonance assignment and protein structure determination
A novel strategy for NMR resonance assignment and protein structure determination
Abstract The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution â?? especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a...
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12-18-2010 01:31 AM
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
J Biomol NMR. 2010 Dec 14;
Authors: Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH
The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed...
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12-17-2010 11:23 AM
[NMR paper] NvAssign: protein NMR spectral assignment with NMRView.
NvAssign: protein NMR spectral assignment with NMRView.
Related Articles NvAssign: protein NMR spectral assignment with NMRView.
Bioinformatics. 2004 May 1;20(7):1201-3
Authors: Kirby NI, DeRose EF, London RE, Mueller GA
MOTIVATION: Nuclear magnetic resonance (NMR) protein studies rely on the accurate assignment of resonances. The general procedure is to (1) pick peaks, (2) cluster data from various experiments or spectra, (3) assign peaks to the sequence and (4) verify the assignments with the spectra. Many algorithms already exist for...
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11-24-2010 09:25 PM
NvAssign: protein NMR spectral assignment with NMRView
NvAssign: protein NMR spectral assignment with NMRView.
http://dir.niehs.nih.gov/dirnmr/nvassign/manual/images/examinePeaks.jpg
Designed by Kirby NI, DeRose EF, London RE, Mueller GA.
Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, NC 27709, USA.
Published in Bioinformatics. 2004 May 1;20(7):1201-3. Epub 2004 Feb 10.
CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMRâ??protein spectral assignment
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