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.
299
datasets available to search
ShareScore release 0.7.1
Dataset results
299 results for “MD simulation”
Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level - MD simulations Dataset
<p>Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks. Systems include all files in GROMACS format needed to reproduce simulations performed in the "Force-tuned Avidity of Spike Variant-ACE2 Interactions viewed on the Single-Molecule Level" article.</p> <p> </p> <table> <caption>Details</caption> <thead> <tr> <th scope="col">system</th> <th scope="col">box size (x-y-z) [nm]</th> <th scope="col">Number of atoms</th> </tr> </thead> <tbody> <tr> <td>Spike +<br> 1x ACE2, full length</td> <td>33.44834 28.96711 57.95573</td> <td>5,665,217</td> </tr> <tr> <td>Spike +<br> 1x ACE2, truncated</td> <td>28.05757 24.29856 46.74417</td> <td>3,203,907</td> </tr> <tr> <td>Spike +<br> 2x ACE2, truncated</td> <td>28.30864 21.23141 48.40873</td> <td>2,936,398</td> </tr> <tr> <td>Spike +<br> 3x ACE2, truncated</td> <td>28.32733 21.24544 48.30436</td> <td>2,936,588</td> </tr> </tbody> </table>
100ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the DES-Amber Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the DES-Amber force field published by Maxwell et al. The simulation was run for 100 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the a99SB-disp force field published by Maxwell et al. The simulation was run for 25 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force field + OpenMM
<p>MD simulation data for the DOPC bilayer with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 DOPC lipids and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
MD Simulation data for a pure POPE bilayer with AMOEBA force field + OpenMM
<p>MD simulation data for the POPE bilayer with the AMOEBA-based force field developed by Li (<a href="https://doi.org/10.1080/00268976.2018.1436201">https://doi.org/10.1080/00268976.2018.1436201</a>).</p> <p>The simulation contains 72 POPE lipids and 2880 water molecules. The trajectory is 305,94 ns long (30594 frames with 10 ps saving frequency).</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the openmm_combined.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. The correction to the timestamp was done via MDAnalysis.</strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p> </p>
RIG-I and RNA complex MD simulations in ff19SB+OL3, ff14SB+OL3, OPLS4 and AMOEBA force fields
<p>MD simulation trajectories of RIG-I variant in complex with RNA. 10*100ns in AMOEBA (a single file from OpenMM), 4*500ns in Amber(ff19sb+OL3, ff14sb+Ol3, polarizable water in amberpol), 4*500ns in Desmond (opls4). </p>
Molecular dynamics (MD) simulations methods and results on cyclooctene oxides in ACN/water hybrid electrolytes
<p><strong>Molecular dynamics (MD) simulations methods and extended results used for the <em>Perspective</em> article entitled</strong></p> <p>“Fine tuning of electrosynthesis pathways by modulation of electrolyte solvation structure”</p>
Snapshots from MD simulations of Yarrowia lipolytica complex I
<p>Simulation snapshots (.pdb) from classical MD of complex I from <em>Yarrowia lipolytica.</em></p> <p>"S" correspond to setups as described in <a href="https://doi.org/10.1016/j.bbabio.2022.148951">https://doi.org/10.1016/j.bbabio.2022.148951</a></p> <p>"R" is replica number and "F" is frame.</p> <p>These files can be visualised in software such as VMD or Pymol.</p>
MD simulations: Conditions for the stable adsorption of lipid monolayers to solid surfaces
<p>Essential files for Gromacs used in the study "Conditions for the stable adsorption of lipid monolayers to solid surfaces."</p> <p>Systems: DLPC bilayer, SAM+DLPC pulling, SAM with water droplets</p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
Triplicate MD simulations performed on the ligand Abscisic acid and the 7CKA protein for a total time of 100 ns.
<p><strong>Molecular Dynamic Simulation study</strong></p> <p>Triplicate MD simulations were performed on the ligand Abscisic acid (<strong>PubChem ID: Abscisic acid</strong>) and the 7CKA protein for a total time of 100 ns. This was done to investigate the quality and stability of the complex until the point at which it converged.</p>
PDB File and MD Simulation results for "The atypical sphingolipid SPB 18:1(14Z);O2 is a biomarker for DEGS1 related hypomyelinating leukodystrophy"
<p>Supplementary structural file for article: "The atypical sphingolipid SPB 18:1(14Z);O2 is a biomarker for DEGS1 related hypomyelinating leukodystrophy":</p> <p>-Predicted Structure of DEGS1 docked to C16 Ceramide in PDB format</p> <p>- 2.5 µsec Molecular Dynamics Simulation of this DEGS1-Ceramide complex embedded in a DPPC membrane and surrounded by TIP3 water and 150 mM NaCl as mp4 (movies) or as original trajectory. In the version with the smaller file size solvent molecules and the membrane are invisible for clarity. </p> <p>Software/Webservices used for generation: AlphaFold, PPM3 web server, CHARM-GUI PDB Manipulator, Maestro/Glide/Ligprep/Desmond (Schrödinger Inc.).</p> <p>Version 1 contained videos in mpeg format that caused error with some players. In Version 2 videos are converted to mp4. </p>
MD simulations of the Sec61/TRAP/ribosome complex Amber force fields
<p>Simulation data for the Sec61/TRAP/ribosome complex embedded in an ER membrane mimic. Simulations are performed using GROMACS and with the all-atom Amber family of force fields. The uploaded trajectory (xtc) contains the coordinates stored every 2 ns of the 2-µs-long simulations. The output energy file (edr), run input file (tpr), and the continue point (cpt) at 2 µs are provided. </p> <p>All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p>
MD simulations of the Sec61/TRAP complex with the Martini 3 force field
<p>Simulation data for the Sec61/TRAP complex, the Sec61 complex, and the TRAP complex in a POPC membrane. Simulations are performed using GROMACS and with the coarse-grained Martini 3 force fields. The proteins are kept restrained in the simulations. The uploaded trajectories (xtc) contain the coordinates stored every 10 ns of the 20-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 20 µs are provided. </p> <p>All required input files are also provided to regenerate the run input files: initial structures (gro), index files (ndx), topologies (top and itp), and the common simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p>
MD simulation of a model Gram-positive bilayer membrane (60% PG, 35% lysyl-PG, 5% CL)
<p><strong>Composition</strong>:</p> <p>Model bilayer composition aimed at replicating the behavior of the Staphylococcus aureus membrane (See also Mohanan et al. Chem Sci 2020, 11, 4669: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159255/"><strong>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159255/</strong></a>)</p> <p>Per leaflet we have 48 POPG (16:0 / 18:1; -1 net charge), 28 DPPGK (16:0 / 16:0; +1 net charge), 4 TOCL1 (18:1,18:1 / 18:1,18:1; -1 net charge), giving 60% PG, 35% lysyl-PG, 5% CL. Bilayer is symmetric. </p> <p><strong>Technical details</strong>:</p> <p>OpenMM 7.5.1</p> <p>CHARMM36m force field</p> <p>6,712 TIP3P waters</p> <p>150 mM KCl (64 K+, 16 Cl-)</p> <p>Temperature = 303.15 K</p> <p>Trajectory output every 100 ps</p> <p>Trajectory length = 500 ns ( = 5,000 frames)</p> <p>(Standard CHARMM-GUI relaxation protocol)</p>
MD simulations data for: Role of the αC-β4 loop in protein kinase structure and dynamics
Open the record for dataset details and reuse information.
MD trajectories for intein simulations
<p>MD simulation trajectories and run files for 400ns simulations for MchDnaB1-HAA. MchDnaB1-HN, and gp41-1WCT-HN inteins. The simulations were run with and without the N-extein sequence.</p>
MD Simulations HsGluN1/GluN2A WT/F553A
<p>Molecular dynamics simulation of the HsGluN1/GluN2A WT and F553A (GluN2A) mutant</p>
LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions, 298K
<p>The last 350ns from a 400ns MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 80:20 (350 POPC, 88 POPG) with Na+ counterions. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx. The starting structure was generated by removing the appropriate number of POPG lipids to get 80:20 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12</p>
LIPID17 POPC-POPG 80:20 MD simulation, Na+ counterions and 100mM CaCl2, 298K
<p>The last 250ns of a 400ns MD simulation trajectory with Amber lipid 17 force field. POPC-POPG 80:20, (350 POPC, 88 POPG), with Na+ counterions and 100mM CaCl2. The starting structure and lipid 17 parameters from here: https://zenodo.org/record/2585523#.Xbf0FC17FBx The starting structure was generated by removing appropriate number of POPG lipids to get 80:20 ratio. Dihedral types are corrected to type 9 as discussed here: https://github.com/NMRLipids/NMRlipidsIVPEandPG/issues/12.</p>
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.