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393 results for “Molecular dynamics simulations”
Molecular Dynamics Simulations of HADDOCK-predicted Complex Structures of apoE2 and Factor H
<p>Input and output data for the molecular dynamics simulations of the FH5–7/ApoE2 complex. Initial structures generated with the HADDOCK v2.4 web server with 3 nm distance restraints for lysine pairs that were experimentally found to be cross-linked with DSS. </p> <p>Five clusters and the four representative structures provided by HADDOCK were then used for atomistic molecular dynamics simulations. These structures were solvated and simulated with both CHARMM36m and Amber FF14SB force fields for 250 ns each using GROMACS 2021. The recommended simulation parameters were used for both force fields, and they are available in the mdp files. </p> <p>For each of these 5 (clusters) x 4 (structures per cluster) x 2 (force fields) = 40 simulations, the outputs and inputs are provided; the trajectory (xtc), energy file (edr), final structure (gro), run parameter file (tpr), and continue point (cpt) are system-specific, whereas a single topology (top) and index file (ndx) is shared among all simulations with the same force field. The molecule definitions (itp) referred to in the topology are provided in the compressed files.</p>
Molecular Dynamics Simulation of CO2 Hydrate Growth in NaCl Aqueous Solution
<p>VIDEO for <a href="https://doi.org/SPE-214332-PA">https://doi.org/SPE-214332-PA</a>17</p>
Dataset I related to publication: Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations
<p>Dataset related to publication:<em> </em></p> <p><em>Leini, R., Kapp, J., Kopra, K. et al. Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations. Sci Rep <strong>15</strong>, 24843 (2025). https://doi.org/10.1038/s41598-025-07532-2</em></p> <ul> <li>.zip-files contain the raw Desmond trajectories of individual replica simulations of GDC-6036.</li> <li>WaterMap-output file for the representative conformation of GDC-6036.</li> </ul>
Dataset II related to publication: Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations
<p>Dataset related to publication:<em> </em></p> <p>Leini, R., Kapp, J., Kopra, K. <em>et al.</em> Binding modes of the KRAS(G12C) inhibitors GDC-6036 and LY3537982 revealed by all atom molecular dynamics simulations. <em>Sci Rep</em> <strong>15</strong>, 24843 (2025). https://doi.org/10.1038/s41598-025-07532-2</p> <ul> <li>.zip-files contain the raw Desmond trajectories of individual replica simulations of LY3537982.</li> <li>WaterMap-output file for the representative conformation of LY3537982</li> </ul>
Molecular dynamics simulation primer for: Introduction to atomistic modeling and simulation of biomolecular systems
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Data from: Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin
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Simulation trajectories from ab-initio molecular dynamics of 4x4x4 super cell of Li3OCl with 4 Li concentrations
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Additional insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity using Supervised Molecular Dynamics Simulations
<p>Adenosine receptors (ARs), like many other G protein-coupled receptors (GPCRs), are targets of primary interest in drug design. However, one of the main limits for the development of drugs for this class of GPCRs is the complex selectivity profile usually displayed by ligands. Numerous efforts have been done for clarifying the selectivity on ARs, leading to the development of many ligand-based models. The structure of the AR subtype A<sub>1</sub> (A<sub>1</sub>AR) has been recently solved, providing important structural insights. In the present work, we rationalized the selectivity profile of two selective A<sub>1</sub>AR and A<sub>2A</sub>AR antagonist investigating their recognition trajectories obtained by Supervised Molecular Dynamics from unbound state and monitoring the role of the water molecules in the binding site.</p>
Figure 3 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 3 Structure of naturally occurring coumarins 13–37 reported possessing antiviral activity.
Figure 2 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 2 Structure of some coumarin drugs 4–13.
Figure 1 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 1 Structure of Aminocoumarin antibiotics Novobiocin, Clorobiocin, and Coumermycin.
Immersion enthalpies of nanomaterials (metals, metal oxides, organic chemistry structures) in water and octanol through molecular dynamics simulations with GROMACS and LAMMPS software
<p>Molecular dynamics simulations (free energy calculations) of water interface properties of spherical and Wulff structures nanoparticles (metals, metal oxides and carbon structures) with GROMACS and LAMMPS software.</p>
Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of tetraglyme-LiTFSI liquid electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of monoglyme-LiTFSI liquid electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations Confined Between Charged Electrodes With Various Surface Charges: Plots
<p>Plots of the data contained in the data sets</p> <ul> <li>Uncharged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165450">https://doi.org/10.5281/zenodo.13165450</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165725">https://doi.org/10.5281/zenodo.13165725</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13166024">https://doi.org/10.5281/zenodo.13166024</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> </ul> </li> <li>Charged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167128">https://doi.org/10.5281/zenodo.13167128</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167338">https://doi.org/10.5281/zenodo.13167338</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167551">https://doi.org/10.5281/zenodo.13167551</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167614">https://doi.org/10.5281/zenodo.13167614</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges</li> </ul> </li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length and electrode surface charge on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 0.25 e/nm², +/- 0.50 e/nm² and +/- 0.75 e/nm². Data for surface charges of +/- 0.00 e/nm² and +/- 1.00 e/nm² are contained in <a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a> and <a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>, respectively.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of charged, graphite-like model electrodes. The model electrodes carry a surface charge of +/- 1.00 e/nm².</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of monoglyme-LiTFSI liquid electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
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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
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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.