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140 results for “molecular dynamics data”
Data supporting Mixed-anion mixed-cation perovskite (FAPbI3)0.875(MAPbBr3)0.125: an ab initio molecular dynamics study
<p>Data of a molecular dynamics simulation of the mixed cation and mixed halide perovskite (FAPbI3)0.875(MAPbBr3)0.125 , as well as the end compounds FAPbI3 and MAPbBr3.</p> <p>Related article: </p> <p><em><strong>J. Mater. Chem. A</strong></em>, 2022,<strong>10</strong>, 9592-9603, <a href="https://doi.org/10.1039/D1TA10860C">https://doi.org/10.1039/D1TA10860C</a></p> <p>arXiv:2112.09795 [cond-mat.mtrl-sci] arXiv: 2112.09795 <a href="https://doi.org/10.48550/arXiv.2112.09795">https://doi.org/10.48550/arXiv.2112.09795</a></p>
Supporting data for:"An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations."
<p>PLUMED_NEST_REPO.zip contains the plumed.dat file and the template PDB used to perform the metainference MD simulations of Gelsolin and UP1-RNA, with and without the Solvation Layer Contribution.</p> <p>TRAJECTORIES.zip contains the Gelsolin and UP1-RNA trajectories and additional data generated with GROMACS. In details:</p> <p>-Gelsolin. Production Molecular Dynamics Parameter file (production.mdp), a topology file (topol.top), and 3 folders: TPRs (with 10 TPR files -one for each replica-), TRJ_SLC_OFF (with data from simulations without Solvation Layer Contribution), and TRJ_SLC_ON (with data from simulations with Solvation Layer Contribution). The last two contain an index file, a trajectory obtained from the concatenation of the 10 replicas (concat.xtc), and a template PDB file.</p> <p>-UP1-RNA. TPR file (md.tpr) and 2 folders: TRJ_SLC_OFF (with data from simulations without solvent correction), and TRJ_SLC_ON (with data from simulations with solvent correction). Each folder contains an index file, a template PDB file and a trajectory file (trj.xtc)</p> <p> </p>
Data from: All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor
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Data from: Molecular and cellular dynamics of the developing human neocortex
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Data from: Salty Sensors, Fresh Ideas: The use of molecular and imaging sensors in understanding plankton dynamics across marine and freshwater ecosystems
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Data from: Synthesis, antimicrobial evaluation, ADMET prediction, molecular docking and dynamics studies of pyridine and thiophene moieties containing chalcones
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Data from: programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations
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Data from: Mapping serotonergic dynamics using drug-modulated molecular connectivity
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Molecular Dynamics Simulations and associated data for: Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases
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Data from: Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations
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Data for: Optimal inference of molecular interaction dynamics in FRET microscopy
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Molecular dynamics simulation data of ELIC in nanodiscs
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Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn-nmr)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn-nmr and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
N-ASW: Molecular Dynamics Data
<ul> <li> Description</li> </ul> <p>The data set was generated from ab-initio molecular dynamics simulations and was used to study the adsorption and desorption dynamics of nitrogen atoms on top of amorphous solid water (ASW) [1]. The data set contains structures with 3 to 378 atoms which result in 28,715 structures in total. The atomization energies and atomic forces are calculated at the PBEh-3c/def2-mSVP level of theory [2]. For more details, see Ref. 1.</p> <ul> <li> Format</li> </ul> <p>The data is stored in python compressed array format (.npz) with the atomization energy in kcal/mol and atomic forces in kcal/mol/Ang. The data set contains five numpy arrays</p> <p>import numpy as np<br> data = np.load('N-ASW.npz')<br> data['R'] # Cartesian coordinates of nuclei (Ang.)<br> data['E'] # Total energy (kcal/mol)<br> data['F'] # Atomic forces (kcal/mol/Ang.)<br> data['N'] # Number of atoms in each structure<br> data['Z'] # Nuclear charges</p> <ul> <li>References</li> </ul> <p>[1] Molpeceres G.; Zaverkin V.; and Kästner J. Neural-Network Assisted Study of Nitrogen Atom Dynamics on Amorphous Solid Water. I. Adsorption & Desorption. Mon. Not. R. Astron. Soc. 2020, submitted<br> [2] Grimme S.; Brandenburg J. G.; Bannwarth C.; Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J. Chem. Phys. 2015, 143, 054107.</p>
Data from: Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics
Non-invasive genetic analysis has been frequently employed to estimate ecological and population parameters for many secretive and/or threatened species. However, Neotropical carnivores have so far been scarcely targeted by such studies. The Neotropical otter (Lontra longicaudis) is a poorly-known species for which local levels of genetic diversity and demographic parameters are virtually absent. We employed non-invasive sampling and amplification of microsatellite loci to investigate population size and density, spatial organization, and relatedness of a wild Neotropical otter population in an Atlantic forest area in southern Brazil. We directly identified 28 individuals and estimate a rather high population density at the study site. Spatial organization analysis indicated that male cumulative displacement was higher than that of females, with the latter sex showing evidence of philopatric behaviour. Also, the reconstruction of genealogical relationships suggests that spatial organization in this otter appears to be influenced by relatedness. By allowing the testing of specific hypothesis targeting these issues, our results provided important glimpses into the Neotropical otter's population biology. Moreover, the findings of the present study reaffirm the power of non-invasive genetics to investigate the biology of this elusive species, and open up new avenues for ecological and demographic studies of other Neotropical carnivores.
Data from: Molecular dynamics simulation of the interaction between palmitic acid and high pressure CO2
<p>In this study, molecular dynamics simulation was used to explore the interaction characteristics of palmitic acid and CO2, and the effects of temperature and pressure on the solubility of palmitic acid in CO2 were investigated. In the range of 293K-353K and 5MPa-30MPa, the snapshot of palmitic acid distribution in CO2 shows that the molecular chain of palmitic acid in high-density CO2 system is more straight and more dispersed than that in low-density CO2 system. The radial distribution function further clearly shows that the solubility of palmitic acid in CO2 decreases with the increase of temperature and increases with the increase of pressure, which is consistent with the fatty acid solubility data reported in the literature and the setting rules of supercritical CO2 extraction process conditions. As the temperature decreases and the pressure increases, the interaction energy between palmitic acid and CO2 increases, which is conducive to overcoming the intermolecular force of palmitic acid and promoting dissolution. The solubility parameters of palmitic acid and CO2 can better reflect the trend of palmitic acid solubility changing with temperature and pressure, which can play a guiding role in the determination of process conditions and even the development of new processes.</p>
MD data for the article "Structure comparison of beta amyloid peptide Aβ 1-42 isoforms. Molecular dynamics modeling" by Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei.
<p>There are CMD and REMD trajectories for Aβ isoforms discussed in the paper together with final coordinate files for these trajectories. The resulting dataset of modeled structures includes wild type Aβ42, isoD7, pS8, D7H and H6R-Aβ42, and wild type Aβ16, isoD7, pS8, D7H and H6R-Aβ16.</p>
Interaction Fingerprints for Molecular Dynamics Simulation of MC-LR and MC-LF with PPP1 - Data
<p>This data sets contains all data to reproduce the conclusions of the following manuscript to analyse, aggregate and visualise interaction fingerprints of Molecular Dynamics Simulation data. </p> <p>S. Jaeger-Honz, K. Klein, F. Schreiber: Systematic Analysis, Aggregation and Visualisation of Interaction Fingerprints for Molecular Dynamics Simulation Data, Journal of Cheminformatics 16 (28), 2024, https://doi.org/10.1186/s13321-024-00822-3.</p> <p>The scripts and libraries necessary to rerun the analysis are published under the following DOI: 10.5281/zenodo.10424417</p> <p> </p>
Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn
<p>Breast cancer has become most prevalent disease and their incidence has doubled in Indian scenario. Targeted therapy with the novel compounds derived from plants could be the promising approach for the development of drugs. <em>Euphorbia thymifolia</em> L is a widely growing tropical herb which has been reported for its various ethnopharmacological properties, including anticancer properties. The aim of the present study was to identify the active phytocompounds present in the methanolic extract using an <em>I</em><em>n-silico</em> approach. The methanolic extract of <em>E. thymifolia</em> (ME.ET) was subjected to GC-MS analysis and the identified compounds were docked with potential protein targets implicated in breast cancer such as ERK1, AKT, EGFR/HER2, ER, MELK, PLK1, PTK6. Compounds with good docking score were further subjected to dynamics study to understand the protein ligand binding stability, ligand pathway calculation, molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculation using Schrodinger suite. Out of 219 unique phytocompounds subjected to docking, two compounds namely, 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino)ethyl 4-isopropylphenyl ester (SADPE) showed good docking score. Molecular dynamics study showed high affinity and low binding energy for TTDB with HER2, ERK1 and SADPE with ER. Hence this is the first study to identify and report active compounds from <em>E.thymifolia</em> linn. Further <em>invitro</em> and <em>invivo</em> anticancer studies can be performed to confirm these results and understand the molecular mechanism by which TTDB and SADPE exhibit anticancer activity against breast cancer.</p>
Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition"
<p>Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition".</p> <p>neutron_data.zip --> neutron data in .nxspe form. S(Q,E) calculated using the DAVE software. Includes logbook spreadsheet. </p> <p>Training_Data.xyz --> xyz file containing training data used to generate Allegro machine learning forcefield in the paper</p> <p>nh3_pimd.deploy --> Trained Allegro model to that can be used in LAMMPS and RXMD software a ML forcefield </p> <p>POSCAR_UNIT_CELL_AMMONIA --> NH3 unit cell in solid phase in POSCAR format that can be read by the VASP software used to perform the DFT simmulations.</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.