Find research datasets worth reusing

Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.

1,084

datasets available to search

ShareScore release 0.9.0

Dataset results

1,084 results for “substrates”

Learn how ShareScore rates datasets ↗

zenodo44/100

The coupling mechanism of ligands with SERT distinguishes substrates from inhibitors (raw data)

Raw data of the manuscript: Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors Abstract: The presynaptic serotonin transporter (SERT) reuptakes the serotonin (5HT) released into the synaptic cleft, thus ensuring temporal and spatial regulation of serotonergic signalling. Clinically approved drugs used for the treatment of neurological disorders, including depression and anxiety modulate SERT by trapping the transporter in the outward-open conformation. Illicit drugs of abuse as amphetamines act as substrates but reverse the transport direction, thereby releasing intracellular accumulated 5HT. Both mechanisms increase extracellular 5HT levels. Stoichiometry of the transport cycle has been described by kinetic schemes, the structures of the main conformations within the transport cycle revealed static coordinates. By combining in-silico approaches with in-vitro experiments and making use of a homologous series of 5HT analogues, we decoded the essential coupling mechanism between the substrate and the transporter which triggers uptake. The free energy calculations showed that only scaffold-bound substrates can correctly close the extracellular gate by pulling on the bundle domain through long-range electrostatic interactions. The associated spatial and physico-chemical requirements define substrate and inhibitor properties, opening new possibilities for rational drug design approaches.

opencc-by-4.0Dec 2022View details →

zenodo44/100

Beyond Substrates: Strain Engineering of Ferroelectric Membranes

Dataset for publication: Beyond Substrates: Strain Engineering of Ferroelectric Membranes D. Pesquera, E. Parsonnet, A. Qualls, R. Xu, A.J. Gubser, J. Kim, Y. Jiang, G. Velarde, Y. Huang, H.Y. Hwang, R. Ramesh, and L.W. Martin, Adv. Mater. 32, 2003780 (2020).   Matlab code for producing Fig.1d, Fig.2a and Fig.4b is given in .txt files

opencc-by-4.0Sep 2020View details →

zenodo44/100

IV-KAPhE kinase-substrate assignments for the entire human phosphoproteome

This data set includes the full, all-vs-all kinase-substrate assignments by the IV-KAPhE method for the entire human phosphoproteome (union of the PhosphoSitePlus human phosphosite database and the Ochoa et al. 2020 high-confidence human phosphoproteome). This is an unfiltered version of Supplemental Table S1 from Invergo BM (2022) "Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data". The data set also includes files to facilitate scoring new human phosphosites, particularly the in vitro half of the IV-KAPhE model. "naive-bayes-plus-model.tar.gz" is an archive of HDF5 files comprising the "Naive Bayes+" multi-label, in vitro kinase-substrate assignment model used in the IV-KAPhE model, as described in the manuscript. These files are to be used with the motif-kit software package and can be used to score new sites. "kinase-int-domains-sig.tsv" and "kinase-sub-domains-sig.tsv" contain Pfam domains enriched among each kinase's interacting partners or substrates, respectively. Finally, "human-kinase-interactions.tsv" and "human-kinase-2nd-interactions.tsv" contain physical interactions and indirect ("2 hop") interactions between human protein kinases and other proteins, as described in the manuscript.

opencc-by-4.0Mar 2022View details →

zenodo44/100

Raw data for the plot in the article entitled "On the electrophoretic deposition of Bi2Te3 nanoparticles through electrolyte optimization and substrate design"

raw data of transport presented in Fig1a of the open access article with the following details: On the electrophoretic deposition of Bi2Te3nanoparticles through electrolyte optimization and substrate design <a href="https://www.sciencedirect.com/journal/colloids-and-surfaces-a-physicochemical-and-engineering-aspects">Colloids and Surfaces A: Physicochemical and Engineering Aspects</a> <a href="https://www.sciencedirect.com/journal/colloids-and-surfaces-a-physicochemical-and-engineering-aspects/vol/649/suppl/C">Volume 649</a>, 20 September 2022, 129537 <a href="https://doi.org/10.1016/j.colsurfa.2022.129537">https://doi.org/10.1016/j.colsurfa.2022.129537</a>

opencc-by-4.0Jun 2022View details →

zenodo44/100

Dataset on substrate-borne vibrations of Constrictotermes cyphergaster (Blattodea: Isoptera) termites

Here we present data on distinct stimuli as elicitors of substrate-borne vibrations performed by worker and soldier termites belonging to the species Constrictotermes cyphergaster (Blattodea: Isoptera: Termitidae: Nasutitermitinae). The study consisted of assays where groups of termites were exposed to different air-borne stimuli and the vibrations thereby elicited were captured by an accelerometer attached under the floor of the arena in which the termites were confined. A video camera was also used as a visual complement. The data provided here contribute to fill a gap currently existing in published datasets on termite communication.

opencc-by-4.0May 2019View details →

zenodo44/100

Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophobic substrate

This dataset contains the output of Molecular Dynamics simulations (MD) of two-phase Couette flow of water/hexane biphasic systems, in terms of density, velocity and temperature fields. Instructions on how to read and analyze the output files in the <code>.tar.gz</code> archives can be found in these previously-published datasets: <a href="https://doi.org/10.5281/zenodo.8077915">https://doi.org/10.5281/zenodo.8077915</a>, <a href="https://doi.org/10.5281/zenodo.6541983">https://doi.org/10.5281/zenodo.6541983</a> The run output files are labeled using the following pattern: <code>hex-ca<capillary-number>-q<partial-charge>.tar.gz</code>. It is possible to obtain the wall speed/contact line speed from the capillary number using the following formula: <code>u_w = U_0*<capillary-number></code>, with <code>U_0 = 37.246 m/s</code>. To reproduce the runs it is necessary to use a specific version of Gromacs that allows for a special algorithm of pressure scaling with position restraints. The code can be obtained by cloning <a href="https://github.com/MicPellegrino/gromacs-flow-field.git">https://github.com/MicPellegrino/gromacs-flow-field.git</a>, and switching to the <code>flow-field-grid-visco-coms-deform</code> branch. The folder <code>conf-wat-hex.zip</code> contains the configuration files to reproduce MD simulations. To prepare the equilibration runs at constant pressure, run after having installed Gromacs: <code>gmx grompp -f npt.mdp -p topology.top -c before-npt.gro -r before-npt.gro -o system-npt.tpr</code> while to prepare the shear runs: <code>gmx grompp -f shear.mdp -p topology.top -c after-npt.gro -r lambda0.gro -rb lambda1.gro -o system-shear.tpr</code> Simulations are launched by running: <code>gmx mdrun -v -s <tpr-file-name>.tpr <possibly-other-mdrun-flags></code> Have fun simulating!

opencc-by-4.0Jan 2024View details →

zenodo44/100

Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophilic substrate

opencc-by-4.0Jan 2024View details →

zenodo44/100

Data on respiration, substrate incorporation, and soil compound concentration in response to simulated root exudation

In this study we used reverse microdialysis to release a mixture of 13C-labeled substrates into intact meadow and forest soil cores (6-hour long) to simulate root exudation. We utilized three different artificial root exudates: sugars (glucose, fructose), organic acids (acetate, succinate), and a combination of sugars and organic acids (glucose, fructose, acetate, succinate); alongside a water-only control for comparison. We collected compounds from soil solutions and measured respiration. Due to 13C-labeled substrate we could differentiate between substrate-derived respiration and SOM-derived respiration. Additionally, we extracted lipid fatty acids from soil and measured their 13C incorporation.

opencc-by-4.0Aug 2024View details →

zenodo44/100

Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters

The input and main output files used for the paper "Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters" are separated in the different tar files depending the MD stage they belong to. Content 00_AlphaFold2: The models predicted from AlphaFold2 01_build_system: The parameters for ATP and the initial pdb file used to build each system 02_minimization: Minimization input files for each variant 03_equilibration: Equilibration input files for each variant 04_long_equilibration: ATP restrained equilibration input files for each variant 05_free_equilibration: Free equilibration input files for each variant 06_production: Free production input files for each variant 07_caver: Caver calculations for each variant and replica 08_transport_tools: Analysis of tunnel networks using TransportTools software 09_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments 10_caverdock: CaverDock calculations for each variant and for each ligand tested 11_membrane_patch: MD simulations for liquiritigenin and POPC membrane only 12_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11 (not for APO). Calculation of X1 and X2 angles for residue N1331 in each variant (not for APO) 13_US_closed_to_open: Umbrella Sampling simulations to obtain the inward facing (IF) open state of each variant. Not used for PMF analysis. 14_US_opening_energy: Umbrella Sampling simulations to obtain the Potential of Mean Force for the transition from IF-closed to IF-open conformations. 15_US_equilibration: Equilibration input files for WT and F562L variants in IF-open states. 16_US_production: Production input files for WT and F562L variants in IF-open states. 17_US_caver: Caver calculations for WT and F562L variants in IF-open states. 18_US_transport_tools: Analysis of tunnel networks using TransportTools software of WT and F562L variants in IF-open states. 19_US_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments for WT and F562L variants in IF-open states. 20_US_caverdock: CaverDock calculations for WT and F562L variants in IF-open states. 21_US_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11. ABC_Sequences.fasta: Sequences from 1KP analysis

opencc-zeroJan 2023View details →

zenodo44/100

Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"

This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article.  If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451).  This dataset is organized in the following folders: Snapshots_Figures_Main_Text.zip, that contains a README.txt file and: - Figure_3 contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man. - Figure_4 contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex. Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside <a href="https://zenodo.org/api/files/f3836540-b7b6-4820-87b3-7fa5dff7840c/Snapshots_Figures_Main_Text.zip">Snapshots_Figures_Main_Text.zip </a>for more information.

opencc-by-4.0Mar 2023View details →

zenodo44/100

Spray impact onto a hot solid substrate: film boiling suppression by lubricant addition. Supplementary Data

This is a Supplementary Data for a paper entitled "Spray impact onto a hot solid substrate: film boiling suppression by lubricant addition" by Gajevic Joksimovic et al. Frontiers in Physics (2023). Data used for plotting of figures Datasets for Fig. 5:  Number at the end of the file name corresponds to the volumetric lubricant concentration used. <ul> <li>      Dataset_Figure5 TimeTemperatatureFlux  Concentration 0.97.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 1.09.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 1.26.txt </li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 1.49.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 1.82.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 2.34.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 3.28.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux Concentration 5.47.txt</li> <li>      Dataset_Figure5 TimeTemperatatureFlux PureWater.txt</li> </ul> Datasets for Fig. 11: <ul> <li>Dataset_Figure11 PHI Omega Omega nu.txt</li> </ul> Supplementary videos The supplementary videos for Fig. 8: <ul> <li>supplementary video Figure8a.mp4</li> <li>supplementary video Figure9b.mp4</li> <li>supplementary video Figure9c.mp4</li> </ul> The supplementary video for Fig. 13 <ul> <li>supplementary video Figure13.mp4</li> </ul>

opencc-by-4.0Feb 2023View details →

zenodo44/100

Data on soil compounds, respiration and incorporation of 13C-labeled substrate

Root exudation increases the concentration of readily available carbon (C) compounds in its immediate environment. This creates ‘hotspots’ of microbial activity characterized by accelerated soil organic matter turnover with direct implications for nutrient availability for plants. However, we still lack a deeper understanding of the microbial metabolic processes that occur in the immediate vicinity of the roots during and after a root exudation event. Even though theoretical concepts have been developed, the direct consequences of root exudation on microbial metabolism and nutrient availability have never been measured in their immediate environment in intact soil. Here, we used reverse microdialysis to simulate root exudation by releasing a 13C-labelled mix of low-molecular-weight organic C compounds at discrete, mm-sized locations in undisturbed soil in combination with 13C stable isotope tracing. This approach allowed us to investigate the fine-scale temporal and spatial response of microbial metabolism and soil chemistry to root exudation at the mm-scale, and to trace microbial respiration and uptake of exuded compounds. Our results show that a 9-hour simulated root exudation pulse leads to i) a large local respiration event and ii) alteration of the temporal dynamics of soil metabolites over the following twelve days right at the spot of exudate release. Notably, we observed an approximately threefold increase in ammonium concentrations twelve hours after the pulse and increased nitrate concentrations five days after the pulse. We also observed an increase of various short-chain fatty acids, such as acetate, propionate and formate over the following days, indicating altered microbial metabolic pathways and activity. Phospholipid and neutral lipid fatty acids (PLFAs and NLFAs) of all major microbial groups were significantly enriched in 13C within a radius of 5 mm around the microdialysis probes, but not beyond. The highest relative 13C enrichment was observed in fungal NLFAs, indicating that a significant proportion of the exuded compounds had been incorporated into fungal storage compounds. Our findings indicate that the punctual release of low-molecular weight organic C compounds into intact soil significantly changes microbial metabolism and activity in its immediate surroundings, which lead to enhanced mineralisation of native organic nitrogen (N). Our observations emphasise the versatility of microbial metabolic pathways that underlie the response of soil microbes to rapidly altered C availability. They furthermore demonstrate the effectiveness of this response, as triggered by root exudation pulses, to increase nutrient availability for plants around the root.

opencc-by-4.0Jul 2023View details →

edi44/100

UCSB SONGS Mitigation Monitoring: Reef Survey - Benthic Algae, Invertebrate, and Substrate Cover

These data describe annual estimates of the percent cover of benthic macroalgae, sessile macroinvertebrates, and hard and soft substrates at three subtidal reefs collected as part of the San Onofre Nuclear Generating Station (SONGS) Mitigation Monitoring Program. Data collection began in 2009 at an artificial reef (Wheeler North Reef in Orange County, CA) and two natural reference reefs (San Mateo Kelp in Orange County, CA and Barn Kelp in San Diego County, CA). In the summer of each year, divers identified and recorded species of sessile algae and macroinvertebrates, and substrate types under twenty uniformly placed points within five 1 m2 quadrats that were uniformly distributed along semi-permanent transects at each reef.

openCC (other)Jun 2025View details →

edi44/100

Final seedling counts for invasive plants seeded at CPCRW on a variety of substrate types.

This dataset contains final seedling counts for invasive plants seeded at the CPCRW research (seeding and measurements taken summer 2012) site on a variety of substrate types.

openOpenFeb 2016View details →

edi44/100

Long-term record of wetted area, substrate type, and plant features in Sycamore Creek, Arizona, USA (2010-2020)

The primary objective of this project is to understand how long-term climate variability and change influence the structure and function of desert streams via effects on hydrologic disturbance regimes. Climate and hydrology are intimately linked in arid landscapes; for this reason, desert streams are particularly well suited for both observing and understanding the consequences of climate variability and directional change. Researchers try to (1) determine how climate variability and change over multiple years influence stream biogeomorphic structure (i.e., prevalence and persistence of wetland and gravel-bed ecosystem states) via their influence on factors that control vegetation biomass, and (2) compare interannual variability in within-year successional patterns in ecosystem processes and community structure of primary producers and consumers of two contrasting reach types (wetland and gravel-bed stream reaches). This dataset was collected to understand changes of biota patch cover in different sites and reaches of Sycamore Creek and the transition of different algal and plant communities in post-flood succession.

openCC0Dec 2020View details →

edi44/100

Substrate Induced Respiration (SIR) from 26 sites across vegetation community gradient in and near sensor network, 2017

In alpine ecosystems, small-scale variations in topography determine the spatial and temporal “patchiness” of snow accumulation, snowmelt, vegetation, and biological activity. In the Niwot Ridge Long-term Ecological Research Program VII proposal, Suding and colleagues specifically articulate a need to determine how asynchronous responses across a landscape affect catchment-scale export of water and nutrients in the context of changing climate (H4). Accordingly, we must develop an understanding of how asynchronous responses in patch-scale behavior including microbial activity and decomposition are connected hydrologically, how they aggregate at the catchment scale, and how those relationships may change in the future. To address this, we measured substrate induced respiration (SIR; analogous to microbial biomass) from alpine tundra soils at 26 locations across a soil moisture and corresponding vegetation community composition gradient that included NWT sensor network nodes 6 through 21 in the Saddle stream catchment. These data help to constrain interactions between patch-scale alpine biogeochemical and hydrological processes over space and time.

openCC (other)Jan 2022View details →

zenodo40/100

Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase

MD trajectories of all-atom and CG simulations of PI4P activated E2P state of the Drs2p-Cdc50p complex.

opencc-by-4.0Jun 2020View details →

zenodo40/100

X-ray diffraction images of yeast 5-aminolevulinic acid dehydratase complexed with substrate 5-aminolevulinic acid.

X-ray diffraction images collected at the BW7B beamline at DESY (Hamburg) on 2 Jun 1998. More details in the notes.

opencc-by-4.0Jan 2017View details →

dryad40/100

Twisted epitaxy of gold nanodiscs grown between twisted substrate layers of molybdenum disulfide

We expand the concept of epitaxy to a regime of "twisted epitaxy" with the epilayer crystal orientation between two substrates influenced by their relative orientation. We annealed nanometer-thick gold (Au) nanoparticles between two substrates of exfoliated hexagonal molybdenum disulfide (MoS2) with varying orientation of their basal planes with a mutual twist angle from 0° to 60°. Transmission electron microscopy studies show that the Au alignment is midway between that of the top and bottom MoS2 when the twist angle of the bilayer is small (< ~7°). For larger twist angles, Au has only a small misorientation with the bottom MoS2 that varies approximately sinusoidally with the twist angle of the bilayer MoS2. Four-dimensional scanning transmission electron microscopy analysis further reveals a periodic strain variation (< |±0.5%|) in the Au nanodiscs associated with the twisted epitaxy, consistent with the Moiré registry of the two MoS2 twisted layers.

opencc-zeroNov 2023View details →

zenodo40/100

FIG. 7 in Spatial Distribution and Substrate Preferences of Bryophyte Species in Mangrove Ecosystems of the East Coast of Marajó Island, Brazil

FIG. 7. — Dendrogram of floristic similarity of the bryophyte flora of mangroves on the Northern and Southeastern coast of Brazil.

opencc-zeroNov 2023View details →

ScienceDex guides

Understand access before you commit

These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated 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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record