Related ArticlesNon-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.
Chemistry. 2015 Jul 28;
Authors: Didenko T, Proudfoot A, Dutta SK, Serrano P, Wüthrich K
Abstract
High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1) H,(1) H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.
PMID: 26227870 [PubMed - as supplied by publisher]
[NMR paper] CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.
CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.
Related Articles CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.
J Biomol NMR. 2015 Apr 28;
Authors: Guerry P, Duong VD, Herrmann T
Abstract
UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved-including signal identification in NMR spectra,...
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04-29-2015 03:49 PM
CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO
CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO
Abstract
UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involvedâ??including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge...
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04-28-2015 12:13 AM
[NMR paper] J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4.
J Biomol NMR. 2014 Nov 27;
Authors: Jaudzems K, Pedrini B, Geralt M, Serrano P, Wüthrich K
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input...
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11-28-2014 11:37 AM
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77Â*% of the backbone assignments, which were interactively validated and extended to 97Â*%. With an input of the near-complete backbone assignments and three 3D...
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11-26-2014 10:50 PM
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
June 2012
Publication year: 2012
Source:Journal of Magnetic Resonance, Volume 219</br>
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Non-uniform weighted sampling (NUWS) is a sampling strategy, related to non-uniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional manner by the...
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02-03-2013 10:13 AM
The J-UNIO protocol for automated protein structure determination by NMR in solution
The J-UNIO protocol for automated protein structure determination by NMR in solution
Abstract The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved -NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first...
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07-05-2012 04:13 AM
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Christopher A. Waudby, John Christodoulou</br>
Non-uniform weighted sampling (NUWS) is a sampling strategy, related to non-uniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional...
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05-01-2012 08:03 PM
[NMR paper] Automation of NMR structure determination of proteins.
Automation of NMR structure determination of proteins.
Related Articles Automation of NMR structure determination of proteins.
Curr Opin Struct Biol. 2004 Oct;14(5):547-53
Authors: Altieri AS, Byrd RA
The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and...
Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.
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