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98 results for “lipid bilayers”
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules. </p>
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
<p>Equilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules. </p>
Trajectory files of ER-like lipid bilayer
<p>Simulation of ER-like lipid bilayer. Including DCD, PSF, and PDB files.</p>
Trajectory file of asymmetric PM-like lipid bilayer
<p>Simulation of asymmetric PM-like lipid bilayer. Including DCD, PSF, and PDB files.</p>
On calculating the bending modulus of lipid bilayer membranes from buckling simulations
<p>Molecular dynamics simulations files that correspond to the buckling simulations method to calculate the bending modulus and the box area fluctuations method to calculate the area compressibility modulus. We performed all molecular dynamics (MD) simulations using the GROMACS software (v. 2016.4) and the MARTINI coarse-grained (CG) force field (v. 2.2), using standard simulation parameters. Each file contains GRO, TOP, ITPs, and MDP files that correspond to the equilibration and the production runs. The name of each folder indicates the types of lipids. We simulate single-component lipid bilayers includes: DLPC, (14:0-14:0), DPPC (16:0-16:0), POPC (16:0-18:1), DOPC (18:1-18:1), PUPC (16:0-22:6), DLiPC (18:2-18:2), DNPC (24:6-24:6), POPG (16:0-18:1), POPS (16:0-18:1), POPE (16:0-18:1), and DPSM (16:0-16:0), and lipid mixtures includes : DOPC:CHOL, DPPC:CHOL, POPC:POPE, DPPC:DLPC, POPC:PUPC, DNPC:DLPC, and DPPC:DLiPC:CHOL, with different molar ratios specified in the folders names. </p>
Pnictogen-Bonding Catalysis Compared to Ion Transport in Lipid Bilayer Membranes: Original Data
<p>Original data underlying the publication. Data are arranged according to the supporting information. </p>
Micelle vesicle lipid bilayer
SciDraw upload
Lipid Bilayer
SciDraw upload
Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress
GEO Series GSE131146. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by array.
Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling
<p>This is the dataset of input files, parameter files and run files for the various protein conformations generated in the study "Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling"</p>
Coarse-grained simulations of cholesterol in symmetric lipid bilayers with restraints on cholesterol positions
<p>Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 2 (DLiPC) or 4 (DAPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2]. In the simulations, a flat-bottom potential was applied to the cholesterol molecules to either prevent them from partitioning to the membrane core, or from performing complete flip–flops.</p> <p>The simulations were run for 10 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>Run parameter files (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 1 ns</li> <li>Energy file (edr) written every 100 ps</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named LLLL_CG_CHOLXX_RR_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid</li> <li>CG stands for coarse-grained (All atom data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>RR is the width of the flat-bottom potential</li> <li>FFF is the tile type (see above)</li> </ul> <p>Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. Moreover, md_RR.mdp is common for both lipid types yet activates a different flat-bottom potential based on RR.</p> <p>[1] <strong>DOI: </strong>10.1021/jp071097f</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
Coarse-grained simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation
<p>Asymmetric membranes consisting of DOPC, cholesterol, and a lipid with a varying level of unsaturation were simulated at 310 K. The DOPC leaflet consisted of 520 molecules, whereas the other leaflet consisted of either 520 DLiPC with 2 double bonds in both chains, 520 DAPC with 4 double bonds in both chains, or 468 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. Additionally, a symmetric DOPC membrane of the same size (520+520 lipids) was simulated. All systems also contained 112 molecules (10 mol%) of cholesterol. The Martini force field [1] was used and the membranes were generated using insane [2].</p> <p>The simulations were run for 50 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>Run parameter files (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 1 ns</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named DOPC_LLLL_CG_CHOLXX_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid in the non-DOPC leaflet</li> <li>CG stands for coarse-grained (All atom data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.</p> <p>[1] <strong>DOI: </strong>10.1021/jp071097f</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
MD simulation trajectory for POPC bilayer with 128 lipid molecules (CHARMM36, Gromacs 5.1)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 5.1.2 with CHARMM36 lipid forcefield.<br> The simulation is composed of 128 POPC at full hydratation and ran for 500ns at 303K, data saved every 10ps.<br> This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation of POPC lipids bilayer at 310K (Berger, Gromacs 3.1.4)
<p>Simulation data and files for POPC Berger simulation at 310K used in publication J. Phys. Chem. B 2007, 111, 3139-3150.</p>
Lipid bilayer stress-activated IRE-1 modulates autophagy during endoplasmic reticulum stress
GEO Series GSE99763. Caenorhabditis elegans. 30 samples. Type: Expression profiling by array.
Lipid bilayer
Drawing uploaded to scidraw.io on: 28 May 2020
Lipid bilayer
Drawing uploaded to scidraw.io on: 28 May 2020
lipid bilayer simplified
SciDraw upload
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International Brain Laboratory public data
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OpenNeuro
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