Metabolomics extensively utilizes Nuclear Magnetic Resonance (NMR) spectroscopy due to its excellent reproducibility and high throughput. Both one-dimensional (1D) and two-dimensional (2D) NMR spectra provide crucial information for metabolite annotation and quantification, yet present complex overlapping patterns which may require sophisticated machine learning algorithms to decipher. Unfortunately, the limited availability of labeled spectra can hamper application of machine learning,...
[NMR paper] NMR metabolomic modeling of age and lifespan: A multicohort analysis
NMR metabolomic modeling of age and lifespan: A multicohort analysis
Metabolomic age models have been proposed for the study of biological aging, however, they have not been widely validated. We aimed to assess the performance of newly developed and existing nuclear magnetic resonance spectroscopy (NMR) metabolomic age models for prediction of chronological age (CA), mortality, and age-related disease. Ninety-eight metabolic variables were measured in blood from nine UK and Finnish cohort studies (N ?31,000 individuals, age range 24-86 years). We used nonlinear...
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04-24-2024 05:58 AM
[NMR paper] Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Proc Natl Acad Sci U S A. 2014 Oct 13;
Authors: Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR
Abstract
The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity...
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10-15-2014 10:58 AM
[NMR paper] VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
Related Articles VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
J Biomol NMR. 2014 Aug 14;
Authors: Nielsen JT, Nielsen NC
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in...
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08-15-2014 12:53 PM
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra
VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in the developmental phase, for data analysis, and for comparison with experimental data. However, existing tools for this purpose can be difficult to use, are sometimes specialized for...
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08-13-2014 07:50 PM
[Question from NMRWiki Q&A forum] simulating 2D-NOESY spectrum from structural model
simulating 2D-NOESY spectrum from structural model
Hello everyoneOur research group planning to study metal-ion induced structural transition using NMR. We are new to this field. Before doing the experiment,we want to do some groundwork. Hence we have an idea of simulating 2D NOESY spectrum of two structural forms of DNA deposited in PDB without any experimental NOE data and curious to know how the spectrum look like. We found out two programs relevant to our idea such as FIRM and CORMA. We started with FIRM because CORMA was a licensed one.Since we are mostly using GNU linux system, FIRM...
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05-06-2014 01:57 AM
[NMR paper] Peakr: Simulating solid-state NMR spectra of proteins.
Peakr: Simulating solid-state NMR spectra of proteins.
Related Articles Peakr: Simulating solid-state NMR spectra of proteins.
Bioinformatics. 2013 Mar 14;
Authors: Schneider R, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M
Abstract
MOTIVATION: When analyzing solid-state NMR spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, e.g., chemical shift predictions and structural...
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03-16-2013 03:18 PM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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02-11-2012 10:31 AM
Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra
Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra
Abstract Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next....
MetAssimulo 2.0: a web app for simulating realistic 1D & 2D Metabolomic 1H NMR spectra
Linear Mode
