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203 results for “NaCl”
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl, Berger force field for lipids and ffgmx for ions
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl (102 POPC, 26 POPS, 4290 WAT, 106 Na+, 80 Cl-). Additional Na+ cations added to neutralize the negative charge of POPS. Berger force field for lipids and ffgmx for ions are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here.</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p> <p> </p>
Data associated to the article "Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study"
<p>Contains input file and data used to generate the figures of the article:</p> <p>Effects of fluoride salt addition to the physico-chemical properties of the MgCl<sub>2</sub>-NaCl-KCl heat transfer fluid : a molecular dynamics study</p> <p>Weiguang Zhou, Yanping Zhang, Mathieu Salanne</p> <p>https://chemrxiv.org/engage/chemrxiv/article-details/618e903a2bf8a950c7d98e5d</p> <p>The files <em>data.inpt</em> and <em>runtime.inpt </em>are used to simulate the system using the software MetalWalls</p> <p>The files <em>MgNaKCl.txt, MgNaKClF01.txt, MgNaKClF05.txt, MgNaKClF10.txt, MgNaKClF20.txt</em> contain the computed densities, viscosities and thermal conductivities at various temperatures for several compositions (provided in the header of the files)</p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Movies of HIV (VLP) particles through 200 nm nanopores (without or with 300mM NaCl)
<p><strong>Soft jamming of viral particles in nanopores</strong><br>Léa Chazot-Franguiadakis, Joelle Eid, Gwendoline Delecourt, Pauline J. Kolbeck, Saskia Brugère,Bastien Molcrette, Marius Socol, Marylène Mougel, Anna Salvetti, Vincent Démery, Jean Christophe Lacroix, Véronique Bennevault, Philippe Guégan, Martin Castelnovo and Fabien Montel.</p> <p>Nature Communications 2024.</p> <p> </p> <p><strong>Description of content:</strong></p> <p>Movies of HIV (VLP) particles through 200 nm nanopores (without or with 300mM NaCl)</p> <p>Dilution of the initial samples (named MM24) by 10, with a resulting concentration of 960.10^5 particles/mL.</p> <p>For each pressure, 4 videos were made (2 of them are shown here). The final sequences are averaged over at least 2 experiments.</p> <p> </p>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)
<p><strong>Title</strong>: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)</p> <p><strong>Description</strong>: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p><strong>MD engine</strong>: gromacs 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310K</p> <p><strong>Simulation time</strong>: 1000ns</p> <p><strong>Saving frequency</strong>: 100ps</p> <p><strong>Molecular content</strong>:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p><strong>Other information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)
<p>System description<br> -------------------<br> - Title: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 2016.1</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 1000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.4</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 2000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> SOL 20470<br> NA 65<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep3)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.1.2</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 5000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_ASPH-CIS) POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K
<p>System description<br> -------------------<br> - Title: (TM3_ASPH-CIS) Simulation POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K membrane</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3_ASPH peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.4</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 2000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_ASPH 10<br> POPC 512<br> SOL 20480<br> NA 55<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * ASP 202 is in protonated form<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 4000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 1000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> CER160 9<br> SOL 34248<br> NA 102<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_ASPH-CIS) Simulation CER160_9_POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation CER160_9_POPC_512_TM3_ASPH_10_5up_5down_NaCl_150mM_310K</p> <p>- Description: Simulation intake nine ceramides (CER16) to a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.5-dev-20150319-0bec922</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 4000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_ASPH 10<br> POPC 512<br> CER160 9<br> SOL 34258<br> NA 92<br> CL 92</p> <p>- Other information:<br> * Simulations containing 9 CER16 in the water phase initially.<br> * Membrane containing LAPTM4B TM3 peptides.<br> * ASP 202 is in protonated form<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
Simulation CER160_50_POPC_512_TM3_D202A_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>XXXXX</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8 mol% ceramide (CER160) and ten LAPTM4B-TM3 peptides with a D202A mutation using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2940 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> TM3_D2A 10<br> POPC 512<br> CER160 50<br> SOL 28090<br> NA 75<br> CL 75</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides with a D202A mutation.</p>
Simulation CER160_50_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> XXXXX</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8 mol% ceramide (CER160) and ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> Gromacs 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2971 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> TM3 10<br> POPC 512<br> CER160 50<br> SOL 28090<br> NA 85<br> CL 75</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p>
Simulation CER160_50_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K (rep1)
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00572</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8 mol% ceramide (CER160) and ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2971 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> TM3 10<br> POPC 512<br> CER160 50<br> SOL 28090<br> NA 85<br> CL 75</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.</p> <p> </p>
Simulation CER160_50_POPC_512_TM3_D202A_10_5up_5down_NaCl_150mM_310K (rep2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>XXXXX</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8 mol% ceramide (CER160) and ten LAPTM4B-TM3 peptides with a D202A mutation using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2913 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> TM3_D2A 10<br> POPC 512<br> CER160 50<br> SOL 28090<br> NA 75<br> CL 75</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides with a D202A mutation.</p>
Simulation CER160_50_POPC_512_NaCl_150mM_310K (rep2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication: </strong>2018</p> <p><strong>DOI publication:</strong> XXXXX</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8% ceramide (CER160) using charmm36 at 310K.</p> <p><strong>MD engine:</strong> Gromacs 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 3496 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 50<br> SOL 28100<br> NA 75<br> CL 75</p>
Simulation CER160_50_POPC_512_NaCl_150mM_310K (rep1) - 10ps trajectory (Part1)
<p><strong>Title publication: </strong><strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></strong></p> <p><strong><strong>Year publication:</strong></strong><strong> 2018</strong></p> <p><strong>DOI publication: XXXXX</strong></p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8% ceramide (CER160) using charmm36 at 310K.</p> <p>Contains Part 1 (0-500 ns) of the trajectory in <a href="https://zenodo.org/deposit/1219494">https://zenodo.org/deposit/1219494 </a>with saving a frequency 10 ps.</p> <p><strong>MD engine:</strong> Gromacs 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1069 ns</p> <p><strong>Saving frequency</strong>: 10 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 50<br> SOL 28100<br> NA 75<br> CL 75</p>
Simulation CER160_50_POPC_512_NaCl_150mM_310K (rep1)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication: </strong>2018</p> <p><strong>DOI publication:</strong> 10.1021/acscentsci.7b00556</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8% ceramide (CER160) using charmm36 at 310K.</p> <p><strong>MD engine:</strong> Gromacs 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1069 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p>(A version with saving frequency of 10 ps can be found in the following links)</p> <ul> <li>https://zenodo.org/deposit/1230317</li> <li>https://zenodo.org/deposit/1230325</li> </ul> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 50<br> SOL 28100<br> NA 75<br> CL 75</p>
Simulation CER160_50_POPC_512_NaCl_150mM_310K (rep1) - 10ps trajectory (Part2)
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00556</p> <p><strong>Description:</strong> Simulation POPC membrane containing ~8% ceramide (CER160) using charmm36 at 310K.</p> <p>Contains Part 2&3 (500-1069 ns) of the trajectory in <a href="https://zenodo.org/deposit/1219494">https://zenodo.org/deposit/1219494 </a>with saving a frequency 10 ps.</p> <p><strong>MD engine:</strong> Gromacs 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1069 ns</p> <p><strong>Saving frequency</strong>: 10 ps</p> <p><strong>Molecular content</strong>:<br> POPC 512<br> CER160 50<br> SOL 28100<br> NA 75<br> CL 75</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.