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1,294 results for “reactions”
Hierarchy of fear: experimentally testing ungulate reactions to lion, African wild dog and cheetah
<p>Experiments have begun demonstrating that the fear (antipredator responses) large carnivores inspire in ungulates can shape ecosystem structure and function. Most such experiments have focused on the impacts of either just one large carnivore, or all as a whole, rather than the different impacts different large carnivores may have in intact multi-predator-prey systems. Experimentally testing the relative fearfulness ungulates demonstrate toward different large carnivores is a necessary first step in addressing these likely differing impacts. We tested the fearfulness ungulates demonstrated to audio playbacks of lions (<em>Panthera leo</em>), African wild dogs (<em>Lycaon pictus</em>), cheetahs (<em>Acinonyx jubatus</em>) or non-predator controls (birds), in Greater Kruger National Park, South Africa. Ungulates ran more to lions than wild dogs and more to wild dogs than cheetahs, demonstrating a very clear hierarchy of fear. Those that did not run were vigilant (looked toward the sound) more upon hearing large carnivores than controls, being most vigilant to lions. Notably, predator prey preferences did not predict the patterns observed. Our results demonstrate that different large carnivores inspire different levels of fear in their ungulate prey, pointing to differing community-level impacts, which we discuss in relation to the ongoing worldwide decline and loss of large carnivores.</p>
Dataset for 'How do the products in methane dehydroaromatization impact the distinct stages of the reaction?'
<p>Dataset for the publication 'How do the products in methane dehydroaromatization impact the distinct stages of the reaction?': https://zenodo.org/record/6341774#.YnPySOhBxhF</p>
Dataset supporting the publication, "Constraints on the role of Laplace pressure in multiphase reactions and viscosity of organic aerosols"
<p>This dataset supports the publication, "Constraints on the role of Laplace pressure in multiphase reactions and viscosity of organic aerosols". This project was funded by the U.S. National Science Foundation Postdoctoral Fellowship Award #AGS-1624696.</p>
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the acylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.</p> <p>RESIDUE LIST:<br> GLY57<br> TYR58<br> SER131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> MOL262</p> <p>VMD selection:<br> (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name CA C O OG CB HA HB2 HB3 HG and resname SER and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA H HA and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name C1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C2 C20 C3 C4 C5 C6 C7 C8 C9 H1 H10 H11 H12 H13 H14 H15 H16 H17 H2 H3 H4 H5 H6 H7 H8 H9 O1 O2 O3 O4 O5 O6 O7 O8 O9 and resname MOL and resid 262)</p> <p>PYMOL selection:<br> (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name CA+C+O+OG+CB+HA+HB2+HB3+HG & resn SER & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+H+HA & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name C1+C10+C11+C12+C13+C14+C15+C16+C17+C18+C19+C2+C20+C3+C4+C5+C6+C7+C8+C9+H1+H10+H11+H12+H13+H14+H15+H16+H17+H2+H3+H4+H5+H6+H7+H8+H9+O1+O2+O3+O4+O5+O6+O7+O8+O9 & resn MOL & resi 262)</p>
Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem
<p>This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules.</p> <p>All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas.</p> <p>All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level.</p> <ul> <li>0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>1.eners.zip: The single point replica energies along all GES-5/IPM pathways.</li> <li>1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways.</li> <li>2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays.</li> <li>3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers.</li> <li>5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like.</li> <li>6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. </li> <li>p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work.</li> <li>README.md: A markdown file that contains additional descriptions.</li> <li>environment.yml: The Conda environment used for the graph-learning. </li> </ul> <p>Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: <a href="https://doi.org/10.1088/2516-1075/ac7993">10.1088/2516-1075/ac7993</a></p>
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design
<p>Training datasets used for LibINVENT publication <a href="https://doi.org/10.1021/acs.jcim.1c00469">https://doi.org/10.1021/acs.jcim.1c00469</a>.</p> <p>The datasets used for training of the prior:</p> <ul> <li><strong>purged_chembl_sliced.smi.gz:</strong> The CHEMBl 27 compounds, filtered according to the rules described in the manuscript and sliced according to the reaction rules.</li> <li><strong>chembl_train.smi.gz:</strong> The purged, sliced dataset used for model training. The DRD2 compounds are removed as described in the manuscript.</li> </ul>
Ancestral environment determines the current reaction to ultraviolet radiation in Daphnia magna
<p><span>An individual's phenotype can be altered by direct contact with its present environment but also by environmental features experienced by previous generations, i.e. parental or grandparental effects. However, the strength and direction of these transgenerational effects may be highly variable according to the ecological conditions experienced by ancestral generations. Here we performed a reciprocal split-brood experiment to compare transgenerational responses to the threat of ultraviolet radiation (UVR) in the zooplankter <em>Daphnia magna</em>, which had, or had not, been exposed to UVR for more than 150 generations, respectively. We found that the environment at which parents and grandparents were reared significantly influenced both behavior and life-history traits of their descendants. However, such transgenerational responses </span><span>differed between <em>D. magna</em> individuals with contrasting ancestral stress history</span><span>, that is, when exposed to UVR previously unexposed individuals rapidly changed their behavior and life-history traits, whereas individuals previously exposed to UVR showed less pronounced response when the UVR threat level relaxed. Hence, we here demonstrate an asymmetric transgenerational plasticity in response to UVR threat. The findings advance our understanding on the evolutionary ecology of such transgenerational effects and their potential role in response to changes in the local environment.</span></p>
On Trapped Modes In Variable White Dwarfs As Probes Of The 12C(α, γ)16O Reaction Rate
<p>The files in this dataset should have everything to re-produce figure 10, the summary plot in the manuscript.</p>
SUM Reaction Data: The Chemoton 2.0 Data Set
<p>This repository contains the data underlying the results presented in Unsleber, J. P.; Grimmel, S. A.; Reiher, M. <strong>2022</strong>, <em>arXiv:2202.13011 [physics.chem-ph]</em>.</p>
dataset How does the balance of metal and acid functions on the benchmark Mo/ZSM-5 catalyst drive the Methane dehydroaromatization reaction
<p>dataset How does the balance of metal and acid functions on the benchmark Mo/ZSM-5 catalyst drive the Methane dehydroaromatization reaction</p>
Dataset for: Locally resolved stress-state in samples during experimental deformation: insights into the effect of stress on mineral reactions
<p>Data used for the publication:<br> Cionoiu, S., Tajčmanová, L., Moulas, E. and Stünitz H. (under review, 2022) Locally resolved stress-state in samples during experimental deformation: insights into the effect of stress on mineral reactions, Journal of Geophysical Research: Solid Earth</p> <p>See details on the files in ReadMe.txt</p>
Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst - XYZ Structure files
<p>XYZ Structures corresponding to DOI: 10.1002/cctc.202200662</p>
Increasing the thermodynamic driving force of the phosphofructokinase reaction in Clostridium thermocellum
<p>Glycolysis is an ancient, widespread, and highly conserved metabolic pathway that converts glucose into pyruvate. In the canonical pathway, the phosphofructokinase (PFK) reaction plays an important role in controlling flux through the pathway. <em>Clostridium thermocellum</em> has an atypical glycolysis and uses pyrophosphate (PPi) instead of ATP as the phosphate donor for the PFK reaction. The reduced thermodynamic driving force of the PPi-PFK reaction shifts the entire pathway closer to thermodynamic equilibrium, which has been predicted to limit product titers. In this work, we replace the PPi-PFK reaction with an ATP-PFK reaction. We demonstrate that the local changes are consistent with thermodynamic predictions: the ratio of fructose 1,6-bisphosphate to fructose-6-phosphate increases, and the reverse flux through the reaction (determined by <sup>13</sup>C labeling) decreases. The final titer and distribution of fermentation products, however, do not change, demonstrating that the thermodynamic constraints of the PPi-PFK reaction are not the sole factor limiting product titer.</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Code availability</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Data availability for polymer measurements</p>
Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface
<p>Data availability of TiO2/SiO2 grid measurements</p>
Coordinates and output files for stationary points determined for the reaction between 1,4-ditrimethylsilyl-1,4-dihydropyridine and unsaturated nitriles.
<p>The .zip folder contains coordinates and output files (containing energies and frequencies) of the different stationary points found for the analyzed reactions, all of them in .xyz format. IRC output files are also included.</p>
Liquid-liquid phase reaction between crystal violet and sodium hydroxide: kinetic study and precipitate analysis
<p>To investigate reaction order and kinetic parameters of the reaction between crystal violet (CV) and sodium hydroxide (NaOH), various concentrations of the reactants were applied. The present work also verifies the unknown solid product produced under highly concentrated conditions. The reaction orders of CV and NaOH were determined to be 1 and 1.17 by pseudo-rate method, respectively, with a rate constant, k, of 0.084 [(M-1.17) s-1]. In addition to pseudo-rate method, the half-life approach is use to calculated the overall reaction order to verify the accuracy of pseudo-rate method. The overall reaction order is determined to be 1.9 by half-life method. Compare reaction order gained from both methods, the overall reaction order is determined as ~2. The precipitate formation was observed when high concentrations of CV (0.01~0.1 M) and NaOH (1.0 M) were applied. Fourier transform infrared (FTIR) spectroscopy was used to compare the spectra of the precipitate generated and a commercial solvent violet 9 (SV9). Based on the FTIR spectra, it was confirmed that the molecular structure of the precipitate matched that of solvent violet 9.</p>
Supporting Information for the Journal Article "The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms"
<p>This dataset contains the supporting information published together with the article "The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms" (<a href="https://doi.org/10.1039/C9FD00061E"><em>Faraday Discuss.</em>, <strong>2019</strong>, <em>220</em>, 443</a>).</p>
Revisiting the paradigm of reaction optimization in flow with a priori computational reaction intelligence
<p>The use of micro/meso-fluidic reactors has resulted in both new scenarios for chemistry and new requirements for chemists. Through flow chemistry, large-scale reactions can be performed in drastically reduced reactor sizes and reaction times. This obvious advantage comes with the concomitant challenge of re-designing long-established batch processes to fit these new conditions. The reliance on experimental trial-and-error to perform this translation frequently makes flow chemistry unaffordable, thwarting initial aspirations to revolutionize chemistry. By combining computational chemistry and machine learning, we have developed a model that provides predictive power tailored specifically to flow reactions. We show its applications to translate batch to flow, to provide mechanistic insight, to contribute reagent descriptors, and to synthesize a library of novel compounds in excellent yields after executing a single set of conditions.</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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.