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.
19
datasets available to search
ShareScore release 0.9.0
Dataset results
19 results for “PME”
Figure 50. Adult male Portia fimbriata from Queensland. The large PME fill a in Neurobiology and vision of jumping spiders (Araneae: Salticidae)
Figure 50. Adult male Portia fimbriata from Queensland. The large PME fill a gap (~20°) between the fields of vision of the ipsilateral PLE and ALE (Land 1985). 2, The irregular-conical, solid angles correponding to the field of vision of each secondary eye are approximated here with sectors of a single plane. Photographs ©JuNrgen Otto, used with permission.
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>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
GROMOS-CKP POPS simulations (versions 1 and 2) 298 K with GROMOS NH3 charges and PME
<p>GROMOS-CKP POPS simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are taken from the standard GROMOS force field parameters. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
GROMOS-CKP DOPS simulations (versions 1 and 2) 303 K with GROMOS NH3 charges and PME
<p>GROMOS-CKP DOPS simulations (303 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are taken from the standard GROMOS force field parameters. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
Slipids POPS simulations (versions 1 and 2) 298 K 1.0 nm cut-off with LJ-PME
<p>Slipids POPS simulations (298 K, starting structure from the CHARMM-GUI) performed with 1.0 nm cut-offs, PME and LJ-PME. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
Slipids DOPS simulations (versions 1 and 2) 303 K 1.0 nm cut-off with LJ-PME
<p>Slipids DOPS simulations (303 K, starting structure from the CHARMM-GUI) performed with 1.0 nm cut-offs, PME and LJ-PME. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
GROMOS-CKP DOPS simulations (versions 1 and 2) 303 K with Berger/Chiu NH3 charges and PME
<p>GROMOS-CKP DOPS simulations (303 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are the same as in the Berger PS simulations (originally taken from the Berger/Chiu PC head group). Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
GROMOS-CKP POPS simulations (versions 1 and 2) 298 K with Berger/Chiu NH3 charges and PME
<p>GROMOS-CKP POPS simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are the same as in the Berger PS simulations (originally taken from the Berger/Chiu PC head group). Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
GROMOS-CKP POPS/POPC simulations (versions 1 and 2) 298 K with GROMOS NH3 charges and PME
<p>GROMOS-CKP POPS/POPC simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed and with 22 POPS and 110 POPC lipids) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are taken from the standard GROMOS force field parameters. Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
GROMOS-CKP POPS/POPC simulations (versions 1 and 2) 298 K with Berger/Chiu NH3 charges and PME
<p>GROMOS-CKP POPS/POPC simulations (298 K, starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed and with 22 POPS and 110 POPC lipids) performed with 1.4 nm cut-offs, PME and a long range dispersion correction. The charges for the NH3 part of the head group are the same as in the Berger PS simulations (originally taken from the Berger/Chiu PC head group). Two different simulations generated with different starting velocities are provided (the files are named v1 and v2 for these different simulations). The trajectories contain only the data from 400-500 ns of the simulations (as per the analysis provided on the nmrlipids blog) and additionally they have been processed with trjconv -skip 10 to keep the upload small.</p>
Pain Modulation Effectiveness (PME)
ClinicalTrials.gov study NCT05783362. IPD Sharing: NO. Countries: 1. Publications: 15.
OpenFF Water Tests w/ LJ-PME (POPC)
Open the record for dataset details and reuse information.
A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq
GEO Series GSE138103. Mus musculus. 60 samples. Type: Expression profiling by high throughput sequencing.
Effect of PME-1 knockout on MEF gene expression
GEO Series GSE242289. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Comparitive Effectiveness of PME Versus Transthoracic Echocardiogram (TTE)
ClinicalTrials.gov study NCT02141269. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Intravitreal Bevacizumab (Avastin) for Pseudophakic Macular Edema (PME)
ClinicalTrials.gov study NCT00406172. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Effect of PME-1 S156A mutant on gene expression of mouse brain
GEO Series GSE254226. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
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.