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.
99
datasets available to search
ShareScore release 0.9.0
Dataset results
99 results for “lipid membrane”
Coordinate files from LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
<p>Coordinate files from the first and last frame of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations used throughout the LipIDens pipeline.</p><p>CG simulations were run for HHAT, OTOP1, ELIC, MscS, TRPV6, ChRmine, Ste2, Connexin-50, NPC1 and the PAT complex. All CG simulations were run for 10 x 15 μs with the exception of NPC1 which was simulated for 10 x 30 μs.</p><p>AT simulations were run for HHAT (5 x 200 ns) and ELIC (3 x 200 ns) in apo configurations.</p><p><strong>File description:</strong></p><p>Directories for each protein are listed with the suffix CG or AT used to indicate the simulation resolution. </p><p>md_fit_firstframe_<i>X</i>.gro - GROMACS structure file for the first frame of replicate <i>X</i>. </p><p>md_fit_lastframe_<i>X</i>.gro - GROMACS structure file for the last frame of replicate <i>X</i>. </p>
Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"
<p><strong>Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"</strong></p> <p>The dataset contains the following folders:</p> <p>- number_of_contacts: files with the number of contacts between the rim domains of LukF and Hlg2 and the membrane, for different bilayer compositions (Fig. 2).</p> <p>- binding_events: files with the duration of the time interavals in which LukF and Hlg2 are bound to the membrane, and the scripts used to compute for each system the number of binding/unbinding events and the average membrane residence time (Fig. 3).</p> <p>- electrostatic_potential: files of the surface electrostatic potential produced with the adaptive Poisson-Boltzmann solver and used for visualization with Chimera (Fig. 4).</p> <p>- angles: files with the angle values computed between the protein axis and the z-axis of the simulation box (Fig. 5).</p> <p>- contacts_per_residue: files with the number of frames in which each protein residue is in contact with the membrane, with respect to the total number of frames in which the rim domain interacts with the bilayer (Fig. 5).</p> <p>- distance_protein_membrane: files with the minimum distance between the protein and the membrane (Fig. 6).</p> <p>- binding_sites: file produced by PyLipid with relevant information on the main DOPC binding sites identified in LukF.</p> <p>- min_distance_per_residue: files with the minimum distance between each protein residue and the membrane, computed at the binding steps (Fig. S5).</p>
Source molecular simulation data for calculating energy and friction profiles and permeability coefficients through model lipid membranes
<p>Energy files from GROMACS molecular dynamics simulations with enhanced free energy sampling contain time-dependent evolution of the free energy profiles and friction profiles (and other energies and simulation properties) that were used for calculating permeability coefficients in the publication https://www.biorxiv.org/content/10.1101/2021.07.16.452599v1</p> <p>Simulation system contains a lipid POPC or DPPC bilayer with a varying amount of cholesterol (specified as mol% in the file name). Hydrophobic level of the permeating particle is specified as "level-I", "level-II" etc. When unspecified in the file name, the particle is hydrophobic level "III". Lipids D-C14-PC denote PC lipids with both tails monounsaturated of length 14 carbon atoms. DOPC is equivalent to D-C18-PC. (Detailed description in the publication)</p> <p>Adaptive Weighted Histogram (AWH) method was used to sample the free energy profile of translocating small molecule through the lipid bilayer.</p> <p>GROMACS tool `gmx awh` reads the files and provides the described profiles.</p> <p>Files were generated by GROMACS `mdrun` simulation engine version 2019.3.</p> <p> </p> <p>Coarse-grained MARTINI 3.0 model was used for modeling the biomolecular interactions.</p> <p>Scripts to perform the simulations and the files with initial configurations and simulation settings are stored in a public GitHub repository depozited on Zenodo.org: <a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p> <p> </p> <p>Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).</p> <p>Lindahl, V., Lidmar, J. & Hess, B. Accelerated weight histogram method for exploring free energy landscapes. J. Chem. Phys. 141, 044110 (2014).</p> <p>Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods 18, 382–388 (2021).</p> <p>Melcr, J. Git repository with analysis scripts for MD simulations of permeability through lipid membranes. (2021) doi:<a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p>
Hyperactive antifreeze protein from the beetle Rhagium mordax stabilizes model lipid membranes during temperature dependent phase transition
<p>Data from the study submitted in the paper Hyperactive antifreeze protein from the beetle Rhagium mordax stabilises model lipid membranes during temperature-dependent phase transition</p> <p>Data Includes;</p> <p>1. DSC results of RmAFPs interactions with liposomes showing Tm, ΔHcal and Full width at half maximum (FWHM) as well as Phase transitions thermographs by DSC on 1.5mg/ml SUV liposomes either with 60μM (or 0.75mg/ml) RmAFPs or without RmAFPs as control.</p> <p>2. fluorescence spectroscopy data, a complete compilation</p>
Data supporting: "Interaction of MRI Contrast Agent [Gd(DOTA)]− with Lipid Membranes: A Molecular Dynamics Study"
Open the record for dataset details and reuse information.
Supplementary Material 1: Phylogenetic tree from Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system
<p>Phylogenetic tree (Black Sea MAGs)</p>
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes? - additional data
<p>CaM_Data_Repository_Revision:<br>This folder contains the experimental raw data, analysis and source for the final figures reported in the paper after revision (Open Biology): "Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?". It is divided into five (1-3) folders, named as the technique used to obtain the data. Each of them, where applicable, consists of three different subfolders (raw data, analysed data, final graph). Read below for more details. </p> <p>1) ConfocalMicroscopy</p> <p> 1a) Raw_Data: the raw images are reported as .dat and .bmp formats, divided into folders (according date first yymmdd, and within the same day according to composition). Each folder contains a .txt file reporting the experimental details </p> <p> 1b) Final_Graph<br> - Figure_1E.csv is the new source file x-y of the bar plot shown in figure 1E (% of GUVs which showed adsorption of CaM over the total amount of measured GUVs) in the revised version of the manuscript<br> <br>2) DLS</p> <p> 2a) Raw Data: <br> - DLS_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - DLS_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 2b) Final_Graph: <br> - Fig.S4B.xlsx contains the x-y source file for the figure S4B<br> - Fig.S5A.xlsx contains the x-y source file for the figure S5A </p> <p>3) Z-potential</p> <p> 3a) Raw Data: <br> - ZetaPotential_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - ZetaPotential_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 3b) Final_Graph: <br> - Fig.S4C.xlsx contains the x-y source file for the figure S4C<br> - Fig.S5B.xlsx contains the x-y source file for the figure S5B </p> <p> </p> <p> </p>
Lipid-polymer nanoparticles to probe the native-like environment of intra-membrane rhomboid protease GlpG and its activity
<p><span>Polymers can facilitate detergent-free extraction of membrane proteins into nanodiscs (e.g., SMALPs, DIBMALPs), incorporating both integral membrane proteins as well as co-extracted native membrane lipids. Lipid-only SMALPs and DIBMALPs have been shown to possess a unique property; the ability to exchange lipids through ‘collisional lipid mixing’<em>.</em> Here we expand upon this mixing to include protein-containing DIBMALPs, using the rhomboid protease GlpG. Through lipidomic analysis before and after incubation with DMPC or POPC DIBMALPs, we show that lipids are rapidly exchanged between protein and lipid-only DIBMALPs, and can be used to identify bound or associated lipids through ‘washing-in’ exogenous lipids. Additionally, through the requirement of rhomboid proteases to cleave intra-membrane substrates, we show that this mixing can be performed for two protein-containing DIBMALP populations, assessing the native function of intramembrane proteolysis and demonstrating that this mixing has no deleterious effects on protein stability or structure</span></p>
Data for publication: Pixelated High-Q Metasurfaces for in Situ Biospectroscopy and Artificial Intelligence-Enabled Classification of Lipid Membrane Photoswitching Dynamics
Open the record for dataset details and reuse information.
Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"
<p>Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. <em>PLoS Comput. Biol.</em> <strong>2023</strong>, <em>19</em>, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.</p>
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from <em>Arabidopsis thaliana </em>is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.</p>
Trajectories of simulated lipid membranes interacting with antimicrobial peptidomimetic AMC-109 and simulation setup files
<p>Trajectories of simulated lipid membranes with antimicrobial peptidomimetic AMC-109.<br> Trajectories are in GROMACS format ".xtc", the frame rate is 10 ns, and water and NaCl ions were omitted from the trajectory deposit to reduce the size to acceptable limits.</p> <p>The molecules are described using MARTINI 3 coarse grained force field.<br> This repository contains a set of simulations with varying ratio of POPC:POPG lipids from<br> 100% POPC, 0% POPG (denoted as "pg000p..") to<br> 0% POPC, 100% POPG (denoted as "pg100p..").<br> Ratios between these two extremes go in steps of 10%,<br> e.g. "pg060p.." denotes 40% POPC, 60% POPG.</p> <p> </p> <p>The files with ".out" or ".xvg" suffix are properties analyzed from the simulation. Namely, they are:<br> - "thickness" : thickness of the membrane<br> - "apl" : area per lipid of the lipid membrane<br> - "numcont" : number of contacts between the peptidomimetic AMC-109 and the lipids<br> - "ordPars" : order parameters of the end tail segments of the sn-1 tail of POPC lipids.</p> <p>More details about how these properties were generated can be found in the attached scripts (".sh" files) in this repository.</p> <p>Sample topology files in GROMACS format (binary ".tpr" and ASCII ".itp") are provided to complete the description of the molecular topologies used to generate the presented simulations.</p> <p> </p> <p>This repository was created as a Supporting Information to a scientific paper at Nature Communications,</p> <p>Lateral membrane organization as target of an antimicrobial peptidomimetic compound, 2023.</p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
Data from: Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments
Open the record for dataset details and reuse information.
Molecular Simulations of Lipid Membrane Partitioning and Translocation by Bacterial Quorum Sensing Modulators
<p>All simulation data and analysis tools for regenerating results from the journal paper:</p> <p>T. Jin, S. J. Patel, and R. C. Van Lehn. “Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators.” <em>PLOS ONE</em>, <strong>accepted.</strong></p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine
<p>Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine</p> <p>NaCl concentration is 730 mM.</p> <p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>the files denoted with 350 resp 700 resp 1000 have NaCl concentrations of 850 resp 1750 resp 2570 mM.</p> <p> </p> <p>The goal was to study the effect of salt on the order parameters of the lipid head group and the glycerol backbone for the NMRlipids project, see http://nmrlipids.blogspot.fi for more information.</p>
Coarse-grained simulations of lipid membranes with various concentrations of embedded proteins
<p>Membranes with a polydisperse set of proteins with lipid/protein ratios of 50 (lp50), 75 (lp75), 100 (lp100), 200 (lp200), and 400 (lp400) are simulated for 100 µs. The protein–protein interactions are scaled down to prevent excessive aggregation. </p> <p>For all simulated lipid/protein ratio, a trajectory (.xtc) file is stored every 10 ns. Note that water beads and ions have been removed for a smaller file size. All beads, including solvent ones, are present in initial and final structures (.gro). Energy terms are stored every 1 ns (.edr). Simulation run input files (.tpr) and checkpoint files (.cpt) enable the rerunning or continuation of the simulations. Topology (.top) and index (.ndx) files for each system are also provided.</p> <p>The topology files for scaled protein–protein interactions work as follows: The bead types of the proteins in their topology files (.itp) are changed to those with a 'p', for example P4–>P4p. The interactions between normal beads are listed in martini_v2.2_standard.itp, while the interactions among 'p' beads as well as the cross terms between 'p' beads and normal beads are given in martini_v2.2_scaled_80.itp. The force constant of the elastic network was increased to enable an integration time step of 20 fs.</p> <p>The lipid head groups are gently restrained in the direction normal to the membrane to prevent excessive fluctuations and they hence simulate the presence of an actin cytoskeleton.</p> <p>The simulation parameters, common for all systems, are listed in the file md.mdp. </p> <p>All files are compatible with Gromacs 5.0.</p> <p>The results extracted from these simulations are presented in the paper</p> <p>M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758</p> <p>The Martini topologies are obtained form http://cgmartini.nl</p>
Maternal omega-3 polyunsaturated fatty acids improved accretion of DHA-enriched phosphatidylethanolamines and neuronal membrane lipid-rich domains in C57BL/6 mice fetal brains during gestation
<p>This file contains raw dataset for fetal brain lipidomics and associated fetal neuronal membrane </p>
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.