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Dataset results
13 results for “NMR shift”
Predicted 13C NMR Chemical Shifts of Natural Products
<p>The Natural Product structures are those from the <a href="https://zenodo.org/record/5336220">COCONUTv5 database</a> .</p> <p>Predictions were obtained by means of the "Check Chemical Shifts" method from <a href="https://www.acdlabs.com/">ACD/Labs</a> C+H NMR Predictors and DB software, version 2020.1.0.</p> <p>The acd_coconut.zip archive contains a single file, acd_coconut.sdf, a collection of 2D structures from COCONUT supplemented by <sup>13</sup>C NMR chemical shifts values from ACD/Labs CNMR Predictor in verification mode.</p> <p>The file mol1.sdf describes the first compound in acd_coconut.sdf and indicates how chemical shift values are encoded.</p> <p>SDF tags related to NMR:</p> <ul> <li><CNMR_SHIFTS> for ACD/Labs DB software</li> <li><Predicted 13C shifts>, <Quaternaries>, <Tertiaries>, <Secondaries>, <Primaries> for <a href="https://sourceforge.net/projects/mixonat/">MixONat</a></li> <li><NMREDATA_ASSIGNMENT>, <NMREDATA_ORIGIN> in the style of <a href="https://nmredata.org/">NMReDATA</a></li> </ul> <p>The calculation workflow is based on tools developped <a href="https://github.com/nuzillard/KnapsackSearch/">here</a>.</p> <p>No attempt was made to change unlikely tautomers (like aliphatic iminols standing for aliphatic amides). Unlikely structures are likely associated to unlikely predicted chemical shift value sets.</p>
Titration_DB: NMR-monitored protein pH titration chemical shift data.
<p>This archive contains a backup of the NMR titration_db database raw chemical shift data.<br> Reference: D. Farrell et al., “Titration_DB: Storage and analysis of NMR-monitored protein pH titration curves.,” Proteins, vol. 78, no. 4, pp. 843–857, 2009.</p> <p>This data was formerly hosted on an interactive website which is no longer active. The files are stored as csv format, one per protein. They are also split into three folders according to the nuclei whose chemical shifts were used to detect the measurement (1H,13C or 15 N). Much of this data was obtained from literature. A table in the zip file (titration_dataset_info.csv) associates the protein name with the original paper. </p> <p>Note that the database stored the pka values fit using a model to each residue dataset. This is not stored here.</p> <p>Also present is a file titdb.fs. This is a binary file that can only be opened using the PEATDB software. PEATDB (Protein Engineering Analysis Tool - Database) was an application for sharing, analysing and storing experimental and theoretical data from Protein Engineering experiments.<br> This is now legacy software and no longer maintained. It was used to allow interactive fitting of the titration data using the Ekin module.<br> It is still possible to install this software if you really need to. It is stored on github at https://github.com/dmnfarrell/peat.</p> <p>D. Farrell May 2019</p>
Chemical shift imaging by NMR metabolomics
<p>This repository contains the point-wise binned NMR spectra as well as the data analysis R-code for the study "Chemical shift imaging by NMR metabolomics using in tube extraction and slice selection." by Silvio Waschina (Kiel University), Karsten Seeger (University of Lübeck).</p>
19F NMR chemical shift and linewidth data of β-arrestin-1
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alfa-synuclein spectra for the paper "Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins"
<p>The experimental data for the paper "Linear discriminant analysis<br> reveals hidden patterns in NMR chemical shifts of intrinsically<br> disordered proteins" - four spectra of an intrinsically disordered<br> protein alfa-synuclein:</p> <p>3D HNCO</p> <p>4D HabCab(CO)NH</p> <p>4D (H)N(CA)CONH</p> <p>4D HNCACO</p> <p>All spectra were acquired using non-uniform sampling (schedules included<br> as 'schedule.txt' files in a format of 'Kozminski' method in VnmrJ). 3D<br> spectrum (HNCO_nuFT.ucsf) was processed using multidimensional Fourier transform<br> (http://nmr.cent3.uw.edu.pl/software, program 'toastd'). Additionally, we provide a spectrum cleaned of NUS artifacts (HNCO_artifacts_cleaned.ucsf) using program handy (http://nmr.cent3.uw.edu.pl/software, program 'handy').</p> <p>4D spectra were processed using sparse multidimensional Fourier transform<br> (http://nmr.cent3.uw.edu.pl/software, program 'reduced'), based on a<br> HNCO peak list ('peak.list' file). Files with processing parameters are<br> included as 'parameters.txt' files.</p> <p>The resulting spectra are included as Sparky .ucsf files. The files for<br> 4D spectra are the collections of 2D cross-sections with the<br> cross-section number corresponding to the numbering of HNCO peaks in the<br> 'peak.list' file.</p> <p>The folder 'Application2_assignment_transfer' contains Sparky 'ucsf' and 'save' files of the two-dimensional NH projection of the HNCO spectrum with the experimental (HSQC_exp.list) and BMRB (HSQC_bmrb.list) peak lists read into the spectrum. The experimental peaks are marked with arbitrary numbers and BMRB peaks - with names of the preceding aa-residues. The correct assignment is shown in the file 'assignment.txt'.</p>
Dataset to publication: ''Magnetstein: An open source tool for quantitative NMR mixture analysis robust to low resolution, distorted lineshapes and peak shifts''
<p>MANIQ (plugin for Mnova 14.3.1 software (Mestrelab Research, S. L., Spain)) and ACD/TP (Targeted Profiling tool for ACD/Spectrus 2020.1.1 (Advanced Chemistry Development, Inc., ACD/Labs Ontario, Toronto, ON, Canada)) project files and raw experimental NMR data to:</p> <table> <caption>Experiments obtained to Magnetstein with optimized parameters, Magnetstein with default parameters, ACD/TP and MANIQ.</caption> <tbody> <tr> <td>Exp. no.</td> <td>Problem</td> <td>Ingredients</td> </tr> <tr> <td>1</td> <td>large intensity differences<br> between peaks</td> <td>α-pinene<br> benzyl benzoate<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>2</td> <td>peak overlap<br> & contamination (extra peaks)</td> <td>imonene<br> α-pinene<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>3</td> <td>low resolution (43 MHz<br> benchtop NMR spectrometer)</td> <td>benzyl benzoate<br> isopropyl myristate<br> limonene<br> pinene</td> </tr> <tr> <td>4</td> <td>lineshape distortion<br> (shim z1 & z2)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> <tr> <td>5</td> <td>peak position<br> mismatch<br> between library<br> and mixture<br> (different<br> temperatures)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> <tr> <td>6</td> <td>test sample</td> <td>α-pinene<br> benzyl benzoate<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>7</td> <td>large intensity<br> differences<br> & peak overlap</td> <td><br> benzyl benzoate<br> m-anisaldehyde<br> (in CDCl<sub>3</sub>)</td> </tr> <tr> <td>8</td> <td><br> peak overlap &<br> different solvents<br> for single<br> ingredients (in CDCl<sub>3</sub>)<br> and mixture (DMSO-d<sub>6</sub>)</td> <td>benzyl benzoate<br> m-anisaldehyde</td> </tr> <tr> <td>9</td> <td>ineshape<br> distortion<br> (shim z2)</td> <td>actate<br> alanine<br> creatine<br> creatinine<br> choline chloride<br> (in D<sub>2</sub>O)</td> </tr> </tbody> </table> <p> </p>
Accurate and Cost-Effective NMR Chemical Shift Predictions for Proteins using Molecules-in-Molecules Fragmentation-Based Method
<p>Files and coordinates associated with the paper titled 'Accurate and Cost-Effective NMR Chemical Shift Predictions for Proteins using Molecules-in-Molecules Fragmentation Based Method. '</p>
Data for Pure Shift NMR in Continuous Flow
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NMR FID for Novel benzothiophene-based fluorescent dye exhibiting a large Stokes shift
<p>FID NMR data for the manuscript "Novel benzothiophene-based fluorescent dye exhibiting a large Stokes shift" published in Synlett</p>
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 9</a> .</p> <p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p> <p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p> <p>File 220916_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/7085063">the LOTUS database version 9</a> and the SMILES chains of the compounds were collected.</p> <p>The SMILES chains were translated to 2D chemical structures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p> <p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p> <p>Each compound was also supplemented with metadata from file 220916_frozen_metadata.csv .</p> <p>Archive file acd_lotusv9.sdf.zip contains acd_lotusv9.sdf with 218,478 compound descriptions inside.</p> <p>Archive file acd_lotusv9.NMRUDB.zip is a compressed version of acd_lotusv9.NMRUDB, itself created by importation of file acd_lotusv9.sdf in an ACD/Labs database file (new with version 0.0.4).</p> <p>The description of the first compound was copied in file firstmolv9.sdf and is provided for a quick inspection of the database content.</p> <p>The title line in firstmolv9.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220916_frozen_metadata.csv .</p> <p>Files acd_lotusv9.sdf acd_lotusv9.NMRUDB contain biological taxonomy data from file 220916_frozen_metadata.csv that were not exploited in acd_lotusv7. Sub-files dealing with a particular taxon can be easily produced now.</p> <p>Chemical shift calculations for <sup>13</sup>C nuclei using the HOSE code approach are available <a href="https://zenodo.org/record/7047760">here</a> for the compounds in acd_lotusv7.</p> <p> </p>
Fig. 5. Linear correlation between the experimental and calculated 13C NMR chemical shifts for 1A and 1B in (±)-hyperzewalsins A D, four pairs of nor-monocyclic polyprenylated acylphloroglucinols with immunosuppressive activity from hypericum przewalskii maxim
Fig. 5. Linear correlation between the experimental and calculated 13C NMR chemical shifts for 1A and 1B.
Chemical shift-based methods in NMR structure determination
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Supporting dataset for "27Al NMR chemical shifts in zeolite MFI via machine learning acceleration of structure sampling and shift prediction"
<p>This dataset includes includes training databases of CHA, MOR and MFI zeolites, trained kernel ridge regression (KRR) models, and the initial structures utilized in the study. A more detailed description of the dataset can be found in the README file.</p> <p>Note, all MD simulations were performed using SiAlOH1 ML potential from the work of Erlebach et al. (Erlebach et al., Nat Commun 15, 4215 (2024)), available at: https://doi.org/10.5281/zenodo.10361794.</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
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DANDI Archive for NWB datasets
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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.