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32 results for “"chemical 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This data was formerly hosted on an interactive website which is no longer active.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>
Rereferenced Chemical Shift files used to select dihedrals for the 5 secondary structure conformations used to calculate Conformational Variability (ConVa).
<p>These Chemical Shifts in this repository were processed with ShiftCrypt (1) and then processed as described in the manuscript. </p> <p> </p> <p>1- Gabriele Orlando, Daniele Raimondi, Luciano Porto Kagami, Wim F Vranken, ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values, <em>Nucleic Acids Research</em>, Volume 48, Issue W1, 02 July 2020, Pages W36–W40, <a href="https://doi.org/10.1093/nar/gkaa391">https://doi.org/10.1093/nar/gkaa391</a></p>
Data set related to the manuscript "Efficient prediction of Nucleus Independent Chemical Shifts for polycyclic aromatic hydrocarbons"
<p>Input/output files for Gaussian calculations, data sets for all plots shown in the manuscript "Efficient prediction of Nucleus Independent Chemical Shifts for polycyclic aromatic hydrocarbons", C code for the NICS calculations through the dipolar model and python code for the NICS calculations through the tight-binding model described in the manuscript.</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>
Climate warming shifts riverine macroinvertebrate communities to be more sensitive to chemical pollutants
<p>Freshwaters are highly threatened ecosystems that are vulnerable to chemical pollution and climate change. Freshwater taxa vary in their sensitivity to chemicals and changes in species composition can potentially affect the sensitivity of assemblages to chemical exposure. Here we explore the potential consequences of future climate change on the composition and sensitivity of freshwater macroinvertebrate assemblages to chemical stressors using the UK as a case study.</p> <p>Macroinvertebrate assemblages under end of century (2080-2100) and baseline (1980-2000) climate conditions were predicted for 608 UK sites for four climate scenarios corresponding to mean temperature changes of 1.28°C to 3.78°C. Freshwater macroinvertebrate toxicity data were collated for 19 chemicals and the hierarchical Species Sensitivity Distribution (hSSD) model was used to predict the sensitivity of untested taxa using relatedness within a Bayesian approach. All four future climate scenarios resulted in shifts in assemblage composition, with increases in the prevalence of molluscan, crustacean and annelid species, and towards increasing insect taxa of Odonata, Chironomidae, and Baetidae species. In contrast decreases in were projected for Plecoptera, Ephemeroptera (except for Baetidae) and Coleoptera species.</p> <p>Shifts in taxonomic composition were associated with changes in the percentage of species at risk from chemical exposure. For the 3.78°C climate scenario, 76% of all assemblages became more sensitive to chemicals and for 18 of the 19 chemicals, the percentage of species at risk increased. Climate warming-induced increases in sensitivity were greatest for assemblages exposed to metals and were dependent on baseline assemblage composition, which varied spatially.</p> <p>Climate warming is predicted to result in changes in the use, environmental exposure and toxicity of chemicals. Here we show that, even in the absence of these climate-chemical interactions, shifts in species composition due to climate warming will increase chemical risk and that the impact of chemical pollution on freshwater macroinvertebrate biodiversity may double or quadruple by the end of the 21st century.</p>
Fig. 1 in 1H, 13C, 15N Chemical Shift Assignments for Mesd12-155
Fig. 1. Pangerpeton sinensis gen. et sp. nov. A. Holotype specimen (IVPP V14244) from Wubaiding Village, Lingyuan City, Liaoning Province, China, probably contemporaneous with the salamander−bearing horizon at Daohugou, Inner Mongolia, Late Jurassic/Early Cretaceous, showing ventral impression of a nearly complete skeleton. B. High−fidelity cast of holotype showing skull, forelimbs and pectoral girdle. C. Line drawing of skull and atlas, taken from cast.
Fig. 2 in 1H, 13C, 15N Chemical Shift Assignments for Mesd12-155
Fig. 2. Fifty percent Majority Rule Consensus of 28 most parsimonious trees resulting from a phylogenetic analysis using PAUP* (see character description in http://spaces.msn.com/members/ywangivpp, and matrix of taxon and character states in Table 2).
Climate warming shifts riverine macroinvertebrate communities to be more sensitive to chemical pollutants
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Data from: Chemical defenses shift with the seasonal vertical migration of a Panamanian poison frog
Dendrobatid poison frogs sequester lipophilic alkaloids from their arthropod prey to use as a form of chemical defense. Some dendrobatid frogs seasonally migrate between the leaf litter of the forest floor in the dry season to the canopy in the wet season, which may yield differences in prey (arthropods) and therefore alkaloid availability over space and time. Here, we document a seasonal vertical migration of Andinobates fulguritus (the yellow-bellied poison frog) from ground to canopy between dry and wet seasons. We observed turnover in alkaloid composition between seasons and found that dry season frogs contained a lower relative quantity of alkaloids; however, there was no change in alkaloid richness between seasons. The 77 alkaloids of 13 structural classes identified in this population appear to be derived mostly from mites and ants, though the two most common alkaloids were mite derived. Our observed shifts in defensive profiles are consistent with well-documented turnover in mite and ant communities between seasons and vertical strata. As climate change is expected to lengthen and strengthen dry seasons in many tropical regions, our results suggest that arboreal poison frogs forced to the ground for longer periods of time may see a shift in the abundance of alkaloids, possibly decreasing their defensive potential. This study provides further predictions for the wide-reaching effects of climate change, even as nuanced as charismatic poison frogs losing their poisons.
19F NMR chemical shift and linewidth data of β-arrestin-1
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Quantitative sodium MRI in foods: addressing sensitivity issues using single quantum Chemical Shift Imaging at high field
<p>Quantitative sodium MRI in foods: addressing sensitivity issues using single quantum Chemical Shift Imaging at high field</p>
Data set related to the manuscript "Understanding the chemical shifts of aqueous electrolyte species adsorbed in carbon nanopores"
<p>Graphical files in the agr format for all the figures in the manuscript entitled "Understanding the chemical shifts of aqueous electrolyte species adsorbed in carbon nanopores". Examples of input files for the density functional theory, lattice and molecular dynamics simulations are also provided.</p>
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>
Processed data for the study on "Observation of site-selective chemical bond changes via ultrafast chemical shifts"
<p>This repository contains the underlying data for the paper entitled "Observation of site-selective chemical bond changes via ultrafast chemical shifts". The uploaded data are preprocessed data measured at the LCLS SLAC facility. Each individual file contains the measurements at a set delay time and spectrometer setting on a shot-by-shot basis.</p> <p>The files contain the following keys:</p> <pre>['Ebeam_energy_MeV', 'Electron_orbit_probe_x', 'Electron_orbit_probe_y', 'Electron_orbit_pump_x', 'Electron_orbit_pump_y', 'Fiducial', 'Fit_quality', 'Gas_monitor_mJ', 'Group', 'N_electrons', 'Photon_energy_FEL_eV', 'Probe_energy_xtcav', 'Probe_pulse_energy_mJ', 'Probe_width_fs', 'Pump_energy_xtcav', 'Pump_pulse_energy_mJ', 'Pump_width_fs', 'TOF_CO_yield', 'TOF_Ne_yield', 'Time_delay_XTCAV']</pre> <p>Description of the individual entries is found in the supplementary materials of the publication. The following table assigns the time delay and measure electron kinetic energy for each dataset.</p> <table> <tbody> <tr> <td>Time delay</td> <td>Ek = 234eV</td> <td>Ek = 220eV</td> <td>Ek = 210eV</td> </tr> <tr> <td>40fs</td> <td>Run_210</td> <td>Run_212</td> <td>Run_213</td> </tr> <tr> <td>20fs</td> <td>Run_231</td> <td>Run_236</td> <td>Run_235</td> </tr> <tr> <td>15fs</td> <td>Run_239</td> <td>Run_242</td> <td>Run_241</td> </tr> <tr> <td>10fs</td> <td>Run_238</td> <td>Run_233</td> <td>Run_234</td> </tr> <tr> <td>5fs</td> <td>Run_228</td> <td>Run_226</td> <td>Run_225</td> </tr> <tr> <td>0</td> <td>Run_221</td> <td>Run_223</td> <td>Run_224</td> </tr> <tr> <td>-5fs</td> <td>Run_217</td> <td>Run_219</td> <td>Run_220</td> </tr> </tbody> </table> <p> </p>
Data for: Conformational Dependence of Chemical Shifts in the Proline Rich Region of TAU Protein
<div> <div> <div> <p>Nuclear magnetic resonance (NMR) is an important method for structure elucidation of proteins, as it is an easy accessible and well understood method. To characterize intrinsically disordered proteins (IDPs) using computational models it is often necessary to analyze and integrate calculated observables with measurements derived from solution NMR experiments.</p> <p>In this case study we investigate whether and which chemical shifts of the proline-rich region of Tau protein (residues 210-240) offer information about the conformational state to distinguish two different microscopic conformers. Using multiple computational methods, chemical shifts of those two conformationally distinct structures are calculated. The different methods are compared regarding their ability to compute chemical shifts that are sensitive to conformational change.</p> <p>The analysis of the data shows significant differences between the available methods and gives suggestions to an improved pathway for ensemble reweighting. Nevertheless, the variation in the chemical shifts which are predicted for configurations that are commonly considered to belong to the same conformation is such that this obscures a comparison between distinct conformations. Conformational sensitivity is found for up to ∼26% of calculated chemical shifts. It is found to be unrelated with atom element and had minor relation with the change of the corresponding φ dihedral angle.</p> </div> </div> </div>
Data from: Chemical defenses shift with the seasonal vertical migration of a Panamanian poison frog
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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>
t1-Noise Elimination by Continuous Chemical Shift Anisotropy Refocusing
<p>Data archived here corresponds to the experimental and simulation data discussed in the Solid-State Nucl. Magn. Reson. paper:<br> "t1-Noise Elimination by Continuous Chemical Shift Anisotropy Refocusing". This includes the recoupling time optimizations and 2D D-HMQC spectra performed using the SR4^2_1, TONE with SR4^2_1 and the CSA-free SR6^3_2 recoupling sequences on 15N-glycine, Y-MOF-76, Histidine hydrochloride, and Al(acac)3, in addition to the SIMPSON simulations of the various sequences as a function of the MAS rate offset.</p>
Data from: Use of an exotic host plant shifts immunity, chemical defense, and viral burden in wild populations of a specialist insect herbivore
<p>Defense against natural enemies constitutes an important driver of herbivore host range evolution in the wild. Populations of the Baltimore checkerspot butterfly, <em>Euphydryas phaeton </em>(Nymphalidae), have recently incorporated an exotic plant, <em>Plantago lanceolata </em>(Plantaginaceae), into their dietary range. To understand the tritrophic consequences of utilizing this exotic host plant, we examined immune performance, chemical defense, and interactions with a natural entomopathogen (Junonia coenia densovirus, <em>Parvoviridae</em>) across wild populations of this specialist herbivore. We measured three immune parameters, sequestration of defensive iridoid glycosides (IGs), and viral infection load in field-collected caterpillars using either <em>P. lanceolata</em> or a native plant, <em>Chelone glabra </em>(Plantaginaceae). We found that larvae using the exotic plant exhibited reduced immunocompetence, compositional differences in IG sequestration, and higher <em>in situ </em>viral burdens compared to those using the native plant. On both host plants, high IG sequestration was associated with reduced hemocyte concentration in the larval hemolymph, providing the first evidence of incompatibility between sequestered chemical defenses and the immune response (i.e., the "vulnerable host" hypothesis) from a field-based study. However, despite this negative relationship between IG sequestration and cellular immunity, caterpillars with greater sequestration harbored lower viral loads. While survival of virus-infected individuals decreased with increasing viral burden, it ultimately did not differ between the exotic and native plants. These results provide evidence that (1) phytochemical sequestration may contribute to defense against pathogens even when immunity is compromised, and (2) herbivore persistence on exotic plant species may be facilitated by sequestration and its role in defense against natural enemies.</p>
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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.
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DANDI Archive for NWB datasets
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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.