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691 results for “Molecular dynamics”
Data related to the article "Molecular dynamics simulations for the prediction of thermophysical properties of plutonium-based molten salts"
<p>Contains input files and data used to generate the figures of the article:</p> <p>Molecular dynamics simulations for the prediction of thermophysical properties of plutonium-based molten salts<br>(Giovanni Pireddu*, Mirella Simoes Santos*, David Lambertin, Timothée Kooyman)<br><br>*:Equal contribution</p> <p>Journal of Nuclear Materials<br>DOI: https://doi.org/10.1016/j.jnucmat.2024.155124</p> <p>The folder EXAMPLE_INPUT_FILES contains typical MetalWalls(https://doi.org/10.21105/joss.02373) (repository(https://gitlab.com/ampere2/metalwalls)) input files used to perform the molecular simulations.</p> <p>The folder DATA_FIGURES contains the processed data used to plot the figures of the paper (see below).</p> <p><br>Figure 2:<br>- 'Fig2_Density.dat' : density as a function of temperature (binary system, calculated from MD simulations)</p> <p>Figure 3:<br>- 'Fig3_HCap.dat' : heat capacity as a function of temperature (binary system, calculated from MD simulations)</p> <p>Figure 4:<br>- 'Fig4_Density.dat' : density as a function of temperature (ternary system, calculated from MD simulations)</p>
Trajectory of DYRK1A-Q17 Complex from 200-ns Molecular Dynamics Simulation
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Molecular Dynamics simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism"
<p>Zipped archives with MD simulation data for the article "Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism" (eLife, accepted).</p>
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
GEO Series GSE120374. Mus musculus. 331 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptome depicts the molecular dynamics of synapse formation in mouse hippocampus
GEO Series GSE212792. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
A dynamic subcutaneous adipose transcriptome of human insulin resistance identifies a molecular predisposition shared with visceral adipose tissue
GEO Series GSE245948. Homo sapiens. 76 samples. Type: Expression profiling by high throughput sequencing.
H3K79me2 dynamics in medium spiny neurons mediate long-term behavioral and cell type-specific molecular effects of early life stress
GEO Series GSE133889. Mus musculus. 69 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics [E. coli]
GEO Series GSE192346. Escherichia coli. 10 samples. Type: Expression profiling by high throughput sequencing.
Investigation on molecular mechanism underlying the dynamic evolution from preneoplasia to invasive lung adenocarcinoma
GEO Series GSE282617. Homo sapiens. 70 samples. Type: Expression profiling by high throughput sequencing.
Acquisition of optimal human follicular helper CD4 T cell function is defined by specific molecular, positional and TCR dynamic signature
GEO Series GSE145418. Homo sapiens. 15 samples. Type: Expression profiling by array.
Molecular_dynamics_input_parameter_and_output_files_NAT2
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Molecular dynamics simulation of human ρ1 GABAA receptor with neurosteriod THDOC
<p>Molecular dynamics simulation trajectory, parameter files for the systems of human ρ1 GABAA receptor with neurosteriod TDHOC.</p>
Molecular dynamics simulation of human ρ1 GABAA receptor with neurosteriod pregnanolone
<p>Molecular dynamics simulation trajectory, parameter files for the systems of human ρ1 GABAA receptor with neurosteriod pregnanolone.</p>
Molecular dynamics simulation of rat EDAA TRPV2 with drugs
<p>Molecular dynamics simulation trajectory, parameter files for the systems of rat EDAA TRPV2 with drugs.</p>
Molecular dynamics simulation dataset
<p>This dataset contains Molecular Dynamics trajectories of 9 endecapeptides, positioned in the pore construct. One trajectory is done in absence of any transolcating peptide.</p> <p>.xtc files correspond to the trajectories and the .gro files contain the corresponding structures, they can be viewed, for example, with VMD.</p> <p>Every trajectory is the concatenation of 8 trajectories, of 125 ns each, which differ for the orientation of the centrai side-chain with respect to the frame of the pore. The following name parts indicate the central residue. The 73-80 files correspond to the construct alone, taken as a reference. </p> <p>1-8 trp; 9-16 tyr; 17-24 arg; 25-32 his; 33-40 glu; 41-48 gln; 49-56 ser; 57-64 ile; 65-72 gly; 73-80 no peptide.</p>
Confusion Matrix - Discrimination from Molecular Dynamics trajectories
<p>One has 10 classes (the 9 endecapeptides + the control). The predictions were done on each data vector using the Random Forest classifier. </p> <p>Rows are the true labels and columns the predicted ones. The values are normalized by the total number of tests.</p> <p>First row would be ARG and of all predictions of the data 66% are true and 34% wrong distributed among the other amino acids as indicated in the cells.</p> <p>Colors are scaled from red (0) to blue (1) followig the values.</p>
Molecular Dynamics simulations (filtered small system)
<p><span>Molecular Dynamics of E. coli ribosomes stalled by the nascent peptide SecM(Ms).</span></p> <p><span>Four systems were simulated: Control, K, N and WT.<span> </span></span></p> <p><span>To facilitate analysis, each system was filtered to include all the residues within 15 Angstroms of the </span><span>nascent chain, including the nascent chain, and the complete tRNA. The resulting structure is shared as a </span><span>pdb file with suffix "within15_tunnel.pdb"</span></p> <p><span>For each system, 5x50 ns trajectories were simulated. </span><span>And the concatenated trajectory is shared (suffix: "within15_concatenated.xtc")</span></p>
Fig. 2 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 2. Formation of tropylium ion with two phenolic –OH groups.
Fig. 3 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 3. (Z)-3-(pentadec-10′-enyl)-catechol structure.
Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction to Fusarium pallidoroseum in melon fruits by the use of pulsed-light
GEO Series GSE256527. Cucumis melo. 18 samples. Type: Expression profiling by high throughput sequencing.
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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.