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535 results for “NMR,”
Towards quantum utility for NMR quantum simulation on a NISQ computer
<p>Included are CSV files to reproduce the plots from the publication "Towards quantum utility for NMR quantum simulation on a NISQ computer" and a jupyter notebook script for plotting. If all files are saved in the same folder it should work immediately. Plotly library is used for plotting.</p>
Raw NMR data for two constructs of the 8-17 DNAzyme in presence of diferent metal ion cofactors.
<p>The provided NMR dataset contains mainly spectra collected for a unimolecular 8-17 DNAzyme construct, featuring shortened substrate-binding arms: 5'-CGC CGG GGT CGA AGA CTG CCA GCG GCT CGA CGG CG-3' (labelled 8-17 short or GTC within the dataset). The spectra are provided for a number of different experimantal conditions:</p> <p>1) in the presence of both Zn2+ and Na+ (conditions used for structure determination)</p> <p>2) in the presence of Zn2+</p> <p>3) in the presence of Na+</p> <p>4) in the presence of Mg2+</p> <p>5) in the presence of Pb2+</p> <p>6) in the presence of both Zn2+ and Na+(Zn2+ titration to a sample initially containing only Na+)</p> <p>In addition 1H NMR titrations were also recorded for the 8-17 DNAzyme construct, used in the previous crystallographic study (labeled 'crystalo' within the dataset). Titrations using Zn2+, Na+, Mg2+ an Pb2+ are provided.</p>
NMR spectroscopy-based metabolomics of organotypic retinal explants
<p>The retina consumes massive amounts of energy, yet its metabolism and substrate exploitation remain poorly understood. Here, we used a murine explant model to manipulate retinal energy metabolism under entirely controlled conditions and utilized <sup>1</sup>H-NMR spectroscopy-based metabolomics, in situenzyme detection, and cell viability readouts to uncover the pathways of retinal energy production. Our experimental manipulations resulted in varying degrees of photoreceptor degeneration, while the inner retina and retinal pigment epithelium were essentially unaffected. This selective vulnerability of photoreceptors suggested very specific adaptations in their energy metabolism. Rod photoreceptors were found to rely strongly on oxidative phosphorylation, but only mildly on glycolysis. Conversely, cone photoreceptors were dependent on glycolysis but insensitive to electron transport chain decoupling. Importantly, photoreceptors appeared to uncouple glycolytic and Krebs-cycle metabolism via three different pathways: 1) the mini-Krebs-cycle, fueled by glutamine and branched-chain amino acids, generating N-acetylaspartate; 2) the alanine-generating Cahill-cycle; 3) the lactate-releasing Cori-cycle. Moreover, the metabolomic data indicated a shuttling of taurine and hypotaurine between the retinal pigment epithelium and photoreceptors, likely resulting in an additional net transfer of reducing power to photoreceptors. These findings expand our understanding of retinal physiology and pathology and shed new light on neuronal energy homeostasis and the pathogenesis of neurodegenerative diseases.</p>
NMR data for "13C-Formate as an Indirect Low-Temperature 1H Lineshape Polarimeter"
<p>NMR data for "13C-Formate as an Indirect Low-Temperature 1H Lineshape Polarimeter".</p> <p>The data enclosed are either NMR data generated by the software TopSpin written by Burker BioSpin or raw text files.</p> <p>The scripts used to analyze the NMR data are available in a next upload.</p> <p>Please refer to the main text of the paper for more details.</p>
Acrylohydrazides derivatives NMR for PeerJ
<p>The raw material provided is intended for publication in ChemRxiv and PeerJ Organic Chemistry. This submission aims to contribute valuable insights to the scientific community within the realm of organic chemistry, fostering collaborative research and advancing our understanding of the field.</p>
Pro-IL-18 NMR and AlphaFold structure coordinate files
<p>Coordinate files for pro-interleukin(IL)-18 are provided. The coordinates were generated from solution NMR structure determination as well as AlphaFold2 and AlphaFold3 predictions.</p>
Data set related to the manuscript "Investigating the effect of particle size distribution and complex exchange dynamics on NMR spectra of ions diffusing in disordered porous carbons through a mesoscopic model"
<p>Graphical files in the agr format for all the figures in the manuscript entitled "Investigating the effect of particle size distribution and complex exchange dynamics on NMR spectra of ions diffusing in disordered porous carbons through a mesoscopic model". XYZ files giving the particles and bulk positions in the lattices are also provided.</p>
Synthesis of 4-Quinolone N-Oxides via Controlled Partial Hydrogenation of 2-Nitrobenzoyl Enamines - NMR Data
<p>This archive contains raw 1H/13C FIDs and associated data in Bruker-specific format that can be viewed with Bruker’s TopSpin or other appropriate NMR processing software. The subfolders are named in accordance with the compound numbering in the associated research paper (Synthesis of 4-Quinolone N-Oxides via Controlled Partial Hydrogenation of 2-Nitrobenzoyl Enamines).</p> <p>Correspondence: angelov@uni-plovdiv.bg</p>
DFT-GIPAW NMR properties of sodium-silicate glasses
<p>DFT-GIPAW calculations (with VASP) of NMR properties of structural models of SiO2-Na2O glasses generated by classical and ab-initio molecular dynamics simulations. The database contains compositions with 10%, 20%, 30%, 40% and 50% mol. Na2O (10Na, 20Na, 30Na, 40Na and 50Na) with 300 atoms and 600 atoms, aiMD models of 700 atoms with 22.5% and 43.1% mol. Na2O (NS22.5 and NS43.1).</p> <p>Structures (300 atoms) have been extracted at 300K, 1000K, 1500K and 2000K (300K.zip, 1000K.zip, 1500K.zip and 2000K.zip) . Models at 300K have been optimized by CP2K before DFT-GIPAW (cellopt.zip). Similarly structures of 600 atoms at 300K and 1000K ( 600at_300K.zip and 600at_1000K.zip) are provided, in addition to aimd structures at 300K (CP2K) ( NS22.5 and NS43.1) aimd.zip and aimd_test.zip.</p> <p>For a detailed description, see DATABASE.pdf.</p> <p>For each composition, ascii files POSCAR , ISOCAR, EFGCAR and EFG_TCAR are provided.</p> <p>POSCAR : standard VASP file</p> <p>ISOCAR, EFGCAR and EFG_TCAR are modified POSCAR-type file with NMR parameters as described in the header line (see file) :</p> <p>ISOCAR: atom (ppm) sigma_iso (Direct) x y z</p> <p>EFGCAR: atom (MHz) Cq nq (Direct) x y z</p> <p>EFG_TCAR: atom V/A2 xx xy xz yx yy yz zx zy zz (Direct) x y z</p> <p> </p>
Supplementary data to the paper "Large scale voxel-based FEM formulation for NMR relaxation in porous media"
<p>This repository contains supplementary data to the paper "Large scale voxel-based FEM formulation for NMR relaxation in porous media", which is being considered for publication. The files are:<br><br>**_data.zip - Binary image files;</p> <p>FEM_T2_**.csv - T2 simulation results using finite elements;</p> <p>FEM_**_inv.csv - T2 inversion for the finite element simulations;</p> <p>RW_T2_**.csv - T2 simulation results using random walk;</p> <p>RW_**_inv.csv - T2 inversion for the random walk simulations;</p> <p>local_digital_correction.c - Vector containing the local geometry correction factors, accessed integers formed by the 8-bit binary key of the node neighborhood;</p> <p>Where ** is the rock type:</p> <p>AC - Austin Chalk</p> <p>BS - Berea Stripe</p> <p>DP - Desert Pink</p> <p>IB - Idaho Brown</p> <p>Obs.: in order to obtain the relaxation curves the following parameters were utilized in the simulations:</p> <p>Bulk diffusivity: 2500 micro-m2/s (all rock samples) </p> <p>Bulk relaxation: 2.6 s (all rock samples)</p> <p>Voxel size: {1.0; 2,0; 0.9; 2.0} micro-m (for AC, BS, DP, IB respectively)</p> <p>Surface relaxivity: {23.3; 12.1; 12.3; 8.3} micro-m/s (for AC, BS, DP, IB respectively)</p>
Figure 3. NMR 13C in Plant metabolite 5-pentadecyl resorcinol is produced by the Amazonian fungus Penicillium sclerotiorum LM 5679
Figure 3. NMR 13C (75 MHz) spectrum of the compound produced by Penicillium sclerotiorum LM 5679.
Attempted Synthesis of the Pseudomonas aeruginosa Metabolite 2-Benzyl-4(1H)-quinolone and Formation of 3-Methylamino-2-(2-nitrobenzoyl)-4H-naphthalen-1-one as an Unexpected Product - NMR Data
<p>This archive contains raw 1H/13C FIDs and associated data in Bruker-specific format that can be viewed with Bruker’s TopSpin or other appropriate NMR processing software. The subfolders are named in accordance with the compound numbering in the associated research paper (Attempted Synthesis of the Pseudomonas aeruginosa Metabolite 2-Benzyl-4(1H)-quinolone and Formation of 3-Methylamino-2-(2-nitrobenzoyl)-4H-naphthalen-1-one as an Unexpected Product).</p> <p>Correspondence: angelov@uni-plovdiv.bg</p> <p> </p>
ddhN biomarkers NMR reference datasets
<p>To visualize the data please click on the following link: <a title="https://zenodo.nmrium.org/zenodo/v1/record/12806559" href="https://zenodo.nmrium.org/zenodo/v1/record/12806559" target="_blank" rel="noopener">https://zenodo.nmrium.org/zenodo/v1/record/12806559</a></p> <p>Reference 1D and 2D spectra from publication: <a href="https://doi.org/10.1021/acs.jproteome.3c00654" target="_blank" rel="noopener">10.1021/acs.jproteome.3c00654</a></p> <p>For further data, please also see zenodo entry: <a href="../doi/10.5281/zenodo.7906157">10.5281/zenodo.7906157</a></p>
5-fluoro-tryptophan USP5 Zf-UBD Growth & Purification for 19F NMR Screening
<p>The expression and purification of USP5<sup>171-290</sup> in media supplemented with 5-fluoro-tryptophan. Mass spectrometry, differential scanning fluorimetry and fluorescence polarization assays were used to verify label incorporation, protein folding and ubiquitin peptide binding respectively. Preliminary 19F NMR experiments were completed with the purified protein to determine if there are perturbations in one of the 19F resonances with a ubiquitin peptide, LRLRGG. </p> <p> </p>
Compounds of interest identified by screening a focused library against USP5 Zf-UBD with a 19F NMR assay
<p>Screening a set of commercial compounds selected from computational docking studies against USP5 zinc finger ubiquitin binding domain (Zf-UBD) using <sup>19</sup>F NMR spectroscopy. You can find details of preliminary <sup>19</sup>F NMR experiments <a href="https://zenodo.org/record/1246807#.WxV8HkgvzIV">here</a>.</p>
Screening Compounds against USP5 Zf-UBD with a 19F NMR assay #2
<p>Screening compounds against USP5 zinc finger ubiquitin binding domain (Zf-UBD) using a <sup>19</sup>F NMR spectroscopy. You can find previous <sup>19</sup>F NMR experiments <a href="https://openlabnotebooks.org/co-crystal-structures-of-usp5-zf-ubd-and-weak-binding-compounds/">here</a>.</p>
Functionalised beta-keto amides NMR Data
<p>This archive contains raw 1H/13C FIDs and associated data in Bruker-specific format that can be viewed with Bruker’s TopSpin NMR software, ACD/NMR Processor, MNova or other appropriate processing software. The subfolders are named in accordance with the compound numbering in the associated research paper ( doi.org/10.3762/bjoc.14.238 ). In addition to the raw data, each subfolder contains processed spectra in ACD/NMR format. Processing includes Fourier transform and where necessary – apodization and phase correction. This was done with ACD/NMR Processor Academic Edition (v. 12.01).</p>
Study on the effects of heterogeneous distribution of methane hydrate on permeability of porous media using low-field NMR technique
<p>Data sets for the Publication 'Study on the effects of heterogeneous distribution of methane hydrate on permeability of porous media using low-field NMR technique' in Water Resources Research.</p>
i-Pr2NMgCl·LiCl Enables the Synthesis of Ketones by Direct Addition of Grignard Reagents to Carboxylate Anions - NMR and HRMS data
<p>Primary raw data for the article published in Organic Letters DOI: 10.1021/acs.orglett.9b02899</p>
Simulated and experimental data distributed to the CASP13 participants in protein structure prediction assisted with sparse NMR data
<p>All simulated and experimental data distributed to the CASP participants in protein structure prediction assisted with sparse NMR data in CASP13.</p> <p>Also available at http://predictioncenter.org/casp13/results.cgi?view=targets&model=first&tr_type=others&sub_type=N&groups_id=</p> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.