Related ArticlesUnified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra.
ACS Chem Biol. 2015 Feb 20;10(2):452-9
Authors: Bingol K, Li DW, Bruschweiler-Li L, Cabrera OA, Megraw T, Zhang F, Brüschweiler R
Abstract
A new metabolomics database and query algorithm for the analysis of (13)C-(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C-(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index . Our new HSQC database separately treats slowly exchanging isomers that belong to the same metabolite, which permits improved query in cases where lowly populated isomers are below the HSQC detection limit. The performance of our new database and query web server compares favorably with the one of existing web servers, especially for spectra of samples of high complexity, including metabolite mixtures from the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on average a 37% higher accuracy (true positive rate) and a 82% lower false positive rate, which makes it a useful tool for the rapid and accurate identification of metabolites from (13)C-(1)H HSQC spectra at natural abundance. This information can be combined and validated with NMR data from 2D TOCSY-type spectra that provide connectivity information not present in HSQC spectra.
[U. of Ottawa NMR Facility Blog] Decoupling in 2D HSQC Spectra
Decoupling in 2D HSQC Spectra
HMQC and HSQC NMR data are commonly used to correlate the chemical shifts of protons and 13C (or 15N) across one chemical bond via the J coupling interaction. The data are 1H detected, with the 1H chemical shift in the horizontal F2 domain and the 13C (or 15N) chemical shift in the vertical F1 domain. In the case of 1H and 13C, the technique depends on protons bonded to 13C. 1H–12C spin pairs provide no coupling information and are suppressed by the method. If one is to observe the 1H signal of a 1H-13C spin pair, one expects to observe a doublet with...
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05-07-2015 12:59 AM
[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...
Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in 15N-13C-ILV methyl labeled proteins
Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in 15N-13C-ILV methyl labeled proteins
Abstract We present a time-shared 3D HSQC-NOESY experiment that enables one to simultaneously record 13C- and 15N-dispersed spectra in Ile, Leu and Val (ILV) methyl-labeled samples. This experiment is designed to delineate the two spectra which would otherwise overlap with one another when acquired together. These spectra display nOe correlations in the detected proton dimension, i.e. with maximum resolution. This is in contrast to NOESY-HSQC types of experiments that...
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01-09-2011 12:46 PM
[NMR paper] A relational database for sequence-specific protein NMR data.
A relational database for sequence-specific protein NMR data.
Related Articles A relational database for sequence-specific protein NMR data.
J Biomol NMR. 1991 Sep;1(3):217-36
Authors: Seavey BR, Farr EA, Westler WM, Markley JL
A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and...
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08-21-2010 11:12 PM
[NMR paper] A relational database for sequence-specific protein NMR data.
A relational database for sequence-specific protein NMR data.
Related Articles A relational database for sequence-specific protein NMR data.
J Biomol NMR. 1991 Sep;1(3):217-36
Authors: Seavey BR, Farr EA, Westler WM, Markley JL
A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and...
Unified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra.
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