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140 results for “molecular dynamics data”
Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation data
<p>Atomistic molecular dynamics simulation data set accompanying manuscript "Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore".</p>
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>
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>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (A47V) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (A47V).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (G46S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (G46S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (F55L) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (F55L).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (F39L) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (F39L).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (D59Y) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (D59Y).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (E76G) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (E76G).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) tetramer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) tetramer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) monomer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) monomer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
Molecular dynamics simulation data of regulatory ACT domain monomer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer mutation (T63P). Simulation setup files are also included. 21 starting conformations are used in simulations. </p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (R68S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (R68S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (T63P).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (L48S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (L48S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (K42I) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (K42I).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65T) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65T).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Supplementary molecular docking and dynamics data of poxin inhibitors of mpox
Open the record for dataset details and reuse information.
Data for the manuscript "Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"
<p>Simulation datasets for manuscript titled "<strong>Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"</strong></p>
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Allen Brain Atlas
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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.