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691 results for “Molecular dynamics”
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with only Na+ counterions (or with K+ counterions when noted with "_KCl" suffix).</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of CaCl2.</p> <p>The numbers in the file names denote the number of additional Ca2+ cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e8V/m, 2e8 V/m, 3e8 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_08.xtc">traj_centered_08.xtc </a>1e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_3_08.xtc">traj_centered_3_08.xtc </a> 3e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_ricentrata_2_08.xtc">traj_ricentrata_2_08.xtc </a> 2e8 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: no field, 2e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_no_field.xtc">traj_centered_no_field.xtc </a> no field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_2_07.xtc">traj_centered_2_07.xtc </a> 2e7 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e7V/m, 5e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p>t<a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_07.xtc?versionId=62da1fac-7265-4aeb-a239-481088fb396a">raj_centered_07.xtc </a> 1e7 V/m</p> <p><a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_5_07.xtc?versionId=c0b8015d-b977-4eda-b678-9d4b719a90e2">traj_centered_5_07.xtc </a> 5e7 V/m</p> <p> </p> <p><br> <br> <br> </p>
Molecular Dynamics Simulation of Aluminium Binding to Amyloid-beta and its Effect on Peptide Structure
<p>MD frames and highest populated clusters, in PDB format</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Supplementary material for "Molecular dynamics gives new insights into the glucose tolerance and inhibition mechanisms on β-glucosidases" (2 video files)
<p>Video S1: MD of the glucose exit in a glucose-tolerant GH1 β-Glucosidase</p> <p>Video S2: Interactions among glucose, D228, K257, and N312 in a glucose-tolerant GH1 β-glucosidase</p>
Molecular dynamics simulation data of the manuscript "KnowVolution of an efficient polyamidase through molecular dynamics simulations of incrementally docked oligomeric substrates"
<p>This repository provides the simulation data as well as the input and parameters files to reproduce our findings.</p> <p><strong>Acknowledgments</strong></p> <p>The authors gratefully acknowledge the computing time provided by RWTH Aachen University. Computations were performed with computing resources granted by RWTH Aachen University under project rwth1584.</p>
Evolution of the conformational dynamics of the molecular chaperone Hsp90
<p>MD snapshots from: "Evolution of the conformational dynamics of the molecular chaperone Hsp90"</p> <p> </p>
Dataset for "Advances in Docking Protocols for PPIs: Insights from AlphaFold2 and Molecular Dynamics Refinement"
<p>Dataset files used in 'Advances in Docking Protocols for PPIs: Insights from AlphaFold2 and Molecular Dynamics Refinement' (https://github.com/SysBioUAB/docking_benchmark)</p>
Molecular dynamics simulation: The process of phosphate transfer from fructose-1,6-bisphosphate to phosphoglycerate mutase 1
<p><span>Molecular dynamics (MD) simulations were performed to investigate the dynamic process of the binding and phosphorylation of PGAM1 by FBP. </span></p>
DFT data from article "Oxide Ion Mobility in V- and P-doped Bi2O3-Based Solid Electrolytes: Combining Quasielastic Neutron Scattering with Ab Initio Molecular Dynamics"
<p>DFT data from article: "Oxide Ion Mobility in V- and P-doped Bi2O3-Based Solid Electrolytes: Combining Quasielastic Neutron Scattering with Ab Initio Molecular Dynamics" (<span><a href="https://pubs.acs.org/doi/full/10.1021/acs.chemmater.2c03103">https://pubs.acs.org/doi/full/10.1021/acs.chemmater.2c03103</a>). Published by 'creators' listed above. </span></p>
Molecular Probes for Tracking Lipid Droplet Membrane Dynamics
<p><strong><span>Abstract</span></strong></p> <p><span>Lipid droplets (LDs) and their membrane proteins play crucial roles in lipid metabolism, signaling, and information transport within cells. LDs feature a unique monolayer lipid membrane that has not been extensively studied due to the lack of suitable molecular probes that are able to distinguish this membrane from the LD lipid core. In this work, we present a three-pronged molecular probe design strategy that combines lipophilicity-based organelle targeting with microenvironment-dependent activation. As a proof-of-concept, we designed an <u>LD</u> <u>m</u>embrane labeling pro-probe called<strong> LDM</strong>, which selectively localizes around LD membranes. Upon activation by the HClO/ClO</span><sup><span>−</span></sup><span> microenvironment that surrounds LDs, <strong>LDM</strong> pro-probe undergoes a color change and releases<strong> LDM-OH</strong> probe that binds to LD membrane proteins. This localizes the probe to the LD-as</span><span>sociated protein space which is restricted to the membrane thus enabling visualization of the ring-like LD membrane. By utilizing<strong> LDM</strong>, we identified the dynamic mechanism of LD membrane contacts and their protein accumulation parameters. Furthermore, using <strong>LDM</strong> in liver cancer cells allowed us to examine the changes in LD/mitochondrial protein accumulation caused by the state of starvation these cells encounter. This led to the discovery that liver cancer cells respond to energy stress during hunger by enhancing LD-mitochondria interactions. Taken together, <strong>LDM</strong> represents the first molecular probe for imaging LD membranes in live cells, and represents an attractive tool for further investigations into the specific regulatory mechanisms and drug discovery associa</span><span>ted with LD related metabolism diseases.</span></p> <p><span> </span></p> <p><em><span>Keywords:</span></em><span> Molecular Imaging, Cancer, Lipid droplets, Super-resolution Imaging</span></p>
Molecular Dynamics of Engineered Hen-Egg Lysozymes
<p>This dataset contains Molecular Dynamics (MD) simulation trajectories of engineered hen-egg lysozymes, stored in DCD format. The simulations were conducted in explicit solvent environments, but water molecules have been excluded from the trajectories for storage. Each trajectory captures the dynamic properties of various engineered lysozyme variants, providing valuable insights into structural changes, stability, and function.</p>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations in the Bulk
<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 salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the bulk.</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> <li>Various plots of the data</li> </ul> <p>The zip archives contain:</p> <ul> <li><code>coiling.zip</code>: MD simulations of single PEO chains in vacuum that were performed to produce coiled PEO chains, which were used to generate the starting structures for the bulk simulations.</li> <li><code>bulk.zip</code>: MD simulations of PEO-LiTFSI polymer electrolytes in the bulk.</li> <li><code>plots.zip</code>: Plots of various structural and dynamic quantities as function of the PEO chain length and the salt concentration.</li> </ul>
Molecular Dynamics Trajectories of Membrane-bound Influenza Hemagglutinin (A/duck/Alberta/35/76) in Complex with 0-3 Copies of FISW84 Fab Fragments
<p>MD simulation trajectories of influenza hemagglutinin (A/duck/Alberta/35/76) in a bilayer mimicking the viral membrane, with 0-3 copies of FISW84 antibody's Fab domains bound.</p> <p>Files are named as (copy number of Fab).(simulation replica ID).(file type extension). The systems were constructed in CHARMM format PSF files and the trajectories were recorded in DCD format.</p> <p>Simulations were performed with NAMD3. The trajectories were re-centered and re-wrapped about the periodic boundary from the raw trajectories, in order to keep the HA-Fab complex and the lipid bilayer appearing as a single continuous entity instead of isolated molecules at the opposite side of the periodic boundary. Water molecules in the simulation were removed in these trajectories due to file size limitations.</p>
Molecular dynamics analysis of iPP-polymorphs; a dataset of alpha and beta atomic structures
<p>This is the dataset corresponding to the publication in the <em>Polymer </em>journal:</p> <p>"Molecular dynamics analysis of iPP-polymorphs; Investigating thermal expansion and elastic properties"</p> <p>Authors:<strong> H.N. Chávez Thielemann, J.A.W. van Dommelen, L.E. Govaert, M. Hütter</strong></p> <p>Year: 2024</p> <p> </p> <p>The dataset presented here provides the chemical structures of iPP crystals, including COMPASS forcefield parameters, as follows:</p> <p>α structures were obtained by repeating the crystalline unit cell 4 times in a, 2 times in b, and 4 times in c (comprising 32 chains and 3456 atoms)</p> <ul> <li><strong><a href="https://zenodo.org/records/14048060/files/alpha2.zip?download=1">alpha2.zip</a>: </strong>α2 is the unit cell with perfect up-down alternation.</li> <li><a href="https://zenodo.org/records/14048060/files/alpha1.zip?download=1"><strong>alpha1.zip</strong></a>: α1 is an α2 but with 50% random up-down alternation.</li> </ul> <p>A X% of regio defects means that X% of the monomers are incorporated with the inverse head-tail order than in a perfect α2 case.<br>Thus, number of atoms and chains remain unvaried.</p> <ul> <li><a href="https://zenodo.org/records/14048060/files/d2p.zip?download=1"><strong>d2p.zip:</strong></a> α2 containing 2% of regio defects.</li> <li><strong><a href="https://zenodo.org/records/14048060/files/d4p.zip?download=1">d4p.zip:</a> </strong>α2 containing 4% of regio defects.</li> </ul> <p>Vacancy, 31 chains, 3348 atoms:</p> <ul> <li><strong><a href="https://zenodo.org/records/14048060/files/v1.zip?download=1">v1.zip:</a> </strong>contains the same α2 but with a vacancy, i.e. a complete chain is missing.</li> </ul> <p>β structures were obtained by repeating the crystalline unit cell 3 times in a, 2 times in b, and 4 times in c (comprising 36 chains and 3888 atoms)</p> <ul> <li><strong><a href="https://zenodo.org/records/14048060/files/beta2.zip?download=1">beta2.zip:</a> </strong>β2 structure is a monochiral domain, with purely right-handed chains.</li> <li><a href="https://zenodo.org/records/14048060/files/beta1.zip?download=1"><strong>beta1.zip:</strong></a> β1 structure comprises twelve left- and twenty-four right-handed chains.</li> </ul> <p> </p> <p>File names ended with <strong>_img</strong> indicates that supplementary images are provided for that structure.</p> <p>In most of the cases, the LAMMPS data files are accompanied by a PDB file for completeness.</p> <p>To download them all including extra files at once, then download the archive file <a href="https://zenodo.org/api/records/14048060/files-archive"><strong>14048060.zip</strong>.</a></p>
Tetramethylammonium–acetate solution molecular dynamics simulations
<p><span>Simulation data used for the publication: "Ion pairing in aqueous tetramethylammonium–acetate solutions by neutron scattering and molecular dynamics simulations".</span></p> <p><span>GROMACS FFMD simulations:</span></p> <ul> <li> <p><span>SI-charmm-full</span></p> </li> <li> <p><span>SI-charmm-ecc85</span></p> </li> <li> <p><span>SI-charmm-ecc75</span></p> </li> <li> <p><span>SI-charmm-lowCH</span></p> </li> <li> <p><span>SI-charmm-lowCO</span></p> </li> <li> <p><span>SI-charmm-highCO</span></p> </li> <li> <p><span>SI-amber-full</span></p> </li> <li> <p><span>SI-amber-ecc85</span></p> </li> <li> <p><span>SI-amber-ecc75</span></p> </li> <li> <p><span>SI-FFMD-for-AIMD-1tma-1acet</span></p> </li> </ul> <p><span>CP2K AIMD simulation: </span></p> <ul> <li> <p><span>SI-AIMD</span></p> </li> </ul>
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Allen Brain Atlas
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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.