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.
669
datasets available to search
ShareScore release 0.9.0
Dataset results
669 results for “ATOM”
Single-atom catalysis in space: Computational exploration of Fischer–Tropsch reactions in astrophysical environments
<p>This supporting material contains:</p> <ul> <li>Cartesian coordinates of the PBE optimized minima and transition states for the reactions under study, in XYZ format.</li> <li>Inputs for the <a href="https://www.cp2k.org/">CP2K</a> and <a href="https://www.crystal.unito.it/">Crystal17</a> packages.</li> <li>Vibrational calculations with all the frequencies.</li> <li>Inputs and outputs for the benchmark study performed with the <a href="https://gaussian.com/">Gaussian16</a> package.</li> </ul>
All-atom MD trajectory TOCL:POPC (20%), 50mM KCl
<p>~400-ns MD simulation of a lipid bilayer, which monolayer was composed of 44 POPC (1-Palmitoyl-2-oleoylphosphatidylcholine) molecules and 6 TLCL (tetra-linoeoyl-cardiolipin) molecules. The background electrolyte is KCl; these ions were added in that amount, which imitates 50-mM ionic force in the bulk. The water amount is large (more than 140 water molecules per lipid), allowing it to equilibrate the electric double layer at a relatively low ionic force.</p> <p>TIP3P water model and CHARMM36 force field were used; the double-deprotonated form of cardiolipin was used (TLCL2). Production simulation was performed with MD integrator (2-fs step, bonds to hydrogen atoms were constrained), Nose-Hoover thermostat (303K, 1-ps time constant) and Parinello-Rahman semi-isotropic barostat (5-ps time constant, water compressibility). PME was used for electrostatics; cut-off radii were set to 1.2 nm. VDW switch radius was set to 1.0 nm.</p> <p>Resulting trajectories deposited:</p> <ul> <li><strong>COMBINED-50ps.trr</strong> [373 ns length, 50-ps step, with velocities]</li> <li><strong>COMBINED-10ps-100ns.trr</strong> [last 100 ns, 10-ps step, with velocities]</li> <li><strong>COMBINED.edr</strong> [373 ns length, 2-ps step]</li> </ul> <p>The additional ZIP archive contains intermediate TPR and MDP files and a force field folder.</p>
All-atom MD trajectory TOCL:POPC (10%), 50mM KCl
<p>500-ns MD simulation of a lipid bilayer, which monolayer was composed of 47 POPC (1-Palmitoyl-2-oleoylphosphatidylcholine) molecules and 3 TLCL (tetra-linoeoyl-cardiolipin) molecules. The background electrolyte is KCl; these ions were added in that amount, which imitates 50-mM ionic force in the bulk. The water amount is large (more than 100 water molecules per lipid), allowing it to equilibrate the electric double layer at a relatively low ionic force.</p> <p>TIP3P water model and CHARMM36 force field were used; the double-deprotonated form of cardiolipin was used (TLCL2). Production simulation was performed with MD integrator (2-fs step, bonds to hydrogen atoms were constrained), Nose-Hoover thermostat (303K, 1-ps time constant) and Parinello-Rahman semi-isotropic barostat (5-ps time constant, water compressibility). PME was used for electrostatics; cut-off radii were set to 1.2 nm. VDW switch radius was set to 1.0 nm.</p> <p>Resulting trajectories deposited:</p> <ul> <li><strong>COMBINED-25ps.trr</strong> [500 ns length, 50-ps step, with velocities] (50, not 25!, <em>filename is improper!</em>)</li> <li><strong>COMBINED-10ps-100ns.trr</strong> [last 100 ns, 10-ps step, with velocities]</li> <li><strong>COMBINED.edr</strong> [500 ns length, 2-ps step]</li> </ul> <p>The additional ZIP archive contains intermediate TPR and MDP files and a force field folder.</p>
All-atom MD trajectory TOCL:POPC (30%), 50mM KCl
<p>500-ns MD simulation of a lipid bilayer, which monolayer was composed of 40 POPC (1-Palmitoyl-2-oleoylphosphatidylcholine) molecules and 10 TLCL (tetra-linoeoyl-cardiolipin) molecules. The background electrolyte is KCl; these ions were added in that amount, which imitates 50-mM ionic force in the bulk. The water amount is large (more than 150 water molecules per lipid), allowing it to equilibrate the electric double layer at a relatively low ionic force.</p> <p>TIP3P water model and CHARMM36 force field were used; the double-deprotonated form of cardiolipin was used (TLCL2). Production simulation was performed with MD integrator (2-fs step, bonds to hydrogen atoms were constrained), Nose-Hoover thermostat (303K, 1-ps time constant) and Parinello-Rahman semi-isotropic barostat (5-ps time constant, water compressibility). PME was used for electrostatics; cut-off radii were set to 1.2 nm. VDW switch radius was set to 1.0 nm.</p> <p>Resulting trajectories deposited:</p> <ul> <li><strong>COMBINED-50ps.trr</strong> [500 ns length, 50-ps step, with velocities]</li> <li><strong>COMBINED-10ps-100ns.trr</strong> [last 100 ns, 10-ps step, with velocities]</li> <li><strong>COMBINED.edr</strong> [500 ns length, 2-ps step]</li> </ul> <p>The additional ZIP archive contains intermediate TPR and MDP files and a force field folder.</p>
All-atomic simulation of DMPC bilayer with PME and with RFZ
<p>We have performed simulations of DMPC to check if the <strong>reaction-field-zero</strong> mode of calculating electrostatics is a good substitute for PME if we want to avoid PME for some reasons (e.g. for stress calculations). We started this simulation from the configuration deposited by Matti Javanainen (10.5281/zenodo.6943413). We performed two simulations of about 500 ns with the same protocol but at 313 K. Protocol for reaction-field-zero is supplemented as well. POPE simulated with the same RFZ protocol is deposited in a separate dataset (10.5281/zenodo.8435138).</p>
All-atom models of SU10 and P68 viral genomes. Supplementary to the "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses".
<p>The dataset contains mmCIF formatted all-atom models of SU10 and P68 viral genomes and the python script used for refinement of the initial MMB-generated coordinates.</p>
All-atomic simulation of POPE bilayer with RFZ
<p>We have performed simulations of POPE to check if the <strong>reaction-field-zero</strong> mode of calculating electrostatics is a good substitute for PME if we want to avoid PME for some reasons (e.g. for stress calculations). We started this simulation from the configuration deposited by Matti Javanainen (10.5281/zenodo.2641987). We performed the simulation of about 500 ns with the reaction-field-zero protocol supplemented as well. DMPC simulated with the same RFZ protocol is deposited in a separate dataset (10.5281/zenodo.8431709).</p>
Safety and Efficacy of Abaloparatide-SC in Men With Osteoporosis (ATOM)
ClinicalTrials.gov study NCT03512262. IPD Sharing: Not stated. Countries: 3. Publications: 3.
Surgical Pain Control With Ropivacaine by Atomized Delivery
ClinicalTrials.gov study NCT01480089. IPD Sharing: NO. Countries: 1. Publications: 10.
Data from: All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor
Open the record for dataset details and reuse information.
Janus Mn single atoms for triggering efficient photothermal catalytic CO2 methanation through spin polarization effect
Open the record for dataset details and reuse information.
Data from: High-throughput computational screening of bioinspired dual atom alloys for CO2 activation
Open the record for dataset details and reuse information.
A scalable realization of local U(1) gauge invariance in cold atomic mixtures
Open the record for dataset details and reuse information.
Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations
Open the record for dataset details and reuse information.
Supplemental data and figures behind: Atomic-scale element and isotopic investigation of 25Mg-rich stardust from a H-burning supernova
Open the record for dataset details and reuse information.
Generalized biomolecular modeling and design with RoseTTAFold all-atom
Open the record for dataset details and reuse information.
A lever hypothesis for Synaptotagmin-1 action in neurotransmitter release and Studies of Synaptotagmin-1 action by all-atom molecular dynamics simulations
Open the record for dataset details and reuse information.
All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex
Open the record for dataset details and reuse information.
Data from: Approaching the standard quantum limit of a Rydberg-atom microwave electrometer
Open the record for dataset details and reuse information.
Observation of mHz-level cooperative Lamb shifts in an optical atomic clock
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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)
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.