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.
19
datasets available to search
ShareScore release 0.9.0
Dataset results
19 results for “bacterial membranes”
Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane models
<p>This dataset presents a comprehensive collection of input data for Molecular Dynamics (MD) simulations performed using the GROMACS simulation software. The included systems cover various membrane environments, each with distinctive properties. The systems consist of:</p> <ol> <li><strong>IM (Inner Membrane):</strong> Simulations involving the bacteral mimicking inner membrane environment.</li> <li><strong>IM_OM (Inner Membrane and Outer Membrane Complex):</strong> Complex systems encompassing both inner and outer bacterial membrane models.</li> <li><strong>OM_D (Double Symmetric Outer Membrane):</strong> Simulations featuring a symmetric outer membrane structure.</li> <li><strong>OM (Asymmetric Outer Membrane):</strong> Simulations with an asymmetric outer membrane configuration.</li> <li><strong>PC Membrane (Phosphatidylcholine Membrane):</strong> Simulations involving membranes composed of phosphatidylcholine.</li> </ol> <p>For each membrane type, the dataset provides three replicas. The dataset includes initial and final structures (.gro files), simulation parameter files (.mdp), index files (.ndx), and topology files (.itp and .top) applicable to all systems. </p>
Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"
<p>This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:</p> <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> <p>Within the OuterMembrane directory, there are 3 primary subdirectories.</p> <ul> <li><strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output</li> <li><strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>)</li> <li><strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.</li> </ul>
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>
Research data for the article "Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity" by Adéla Melcrová, Christiaan Klein, and Wouter Roos, Nano Letters 2024.
<p>Research data for the publication Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity, Nano Letters, 2024. <a href="https://doi.org/10.1021/acs.nanolett.4c01873" target="_blank" rel="noopener">https://doi.org/10.1021/acs.nanolett.4c01873</a></p> <p>The data set contains experimental data on the study of antimicrobial N-alkylamide 3d and its interaction with the membrane extracted from the bacteria Staphylococcus aureus. Experimental details can be found in the Methods section of the Supporting Information of the mentioned article. </p> <p>The data set contains underlying data for each Figure in the publication including the figures in the Supporting Information. </p> <ul> <li>Figure 1, S2, S3, S6, S8 - Atomic Force Microscopy images in the raw format as collected on JPK Nano Wizard Ultra Speed AFM.</li> <li>Figure 2, 3, S1 - High-Speed Atomic Force Microscopy images in the raw format as collected on high-speed AFM RIBM machine. The data could be opened in Kodec software. The full trajectories recorded on the high-speed AFM machine are presented here. Only snapshots were used in the publication Figures.</li> <li>Figure S7, S9 - Snapshots from the High-Speed AFM measurements showing the cross-section lines (.bmp) together with the cross-section profiles (.csv) that were used to measure the height of supramolecular structures on top of the bacterial membrane.</li> <li>Data underlying Figure S5 and Supporting Video 1 overlap with the data presented in Figure 2a.</li> </ul>
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>
Data for "Coordination of bacterial cell wall and outer membrane biosynthesis"
<p>Raw data used in the paper "Coordination of bacterial cell wall and outer membrane biosynthesis" by Katherine R. Hummels, Samuel P. Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K. Min, Suzanne Walker, Debora S. Marks, and Thomas G. Bernhardt. These data were collected with the aim of understanding how the lipopolysaccharide biosynthetic enzyme LpxC is regulated in diverse gram-negative bacteria, particularly Pseudomonas aeruginosa. The dataset contains the following tarred directories:</p> <p><em><strong>Experimental data</strong></em></p> <ul> <li>Microscopy (microscopy.tar.gz)</li> <li>LC-MS/MS (lc-ms_ms.tar.gz)</li> </ul> <p><strong><em>Covariation analysis</em></strong></p> <ul> <li>Multiple sequence alignments (alignments.tar.gz)</li> <li>AlphaFold structures (alphafold.tar.gz)</li> <li>EVcomplex models and couplings (evcomplex.tar.gz)</li> <li>Phylogenetic trees (trees.tar.gz)</li> </ul> <p>For more detailed methods and file descriptions, please see README.md. Associated code for analysis can be found at https://github.com/samberry19/evcomplex-interaction-scoring.</p>
Detoxified J5 Core Glycolipid/ Group B Meningococcal Outer Membrane Protein Vaccine for Gram-negative Bacterial Sepsis Administered With and Without Synthetic CPG Oligodeoxynucleotide 7909 Adjuvant
ClinicalTrials.gov study NCT01164514. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Membrane Vesicles of a Bacterial Mutualist Mediate Immune Regulation via Dendritic Cells
GEO Series GSE39563. Mus musculus. 4 samples. Type: Expression profiling by array.
Bacterial membrane phosphatidylglycerols activate a population of human CD1a-restricted t cells
GEO Series GSE186459. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Nanobody engineered and photosensitiser loaded bacterial outer membrane vesicles potentiate anti-tumor immunity and immunotherapy
GEO Series GSE272295. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Using small RNA-Seq to identify differential small RNA content of bacterial outer membrane vesicles (OMVs) secreted by Pseudomonas aeruginosa in response to tobramycin exposure
GEO Series GSE183895. Pseudomonas aeruginosa. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide identification of bacterial membrane protein expression determinants
GEO Series GSE95857. Escherichia coli BW25113. 94 samples. Type: Other.
A highly conserved bacterial effector localizes to the host plasma membrane and downregulates the expression of the NDR/HIN1-like 13 (NHL13) gene requiried for antibacterial immunity in Arabidopsis
GEO Series GSE67179. Arabidopsis thaliana. 15 samples. Type: Expression profiling by array.
small RNA-Seq showing transfer of bacterial outer membrane vesicle (OMV) sRNA to host airway epithelial cells
GEO Series GSE80421. Homo sapiens; Pseudomonas aeruginosa. 10 samples. Type: Expression profiling by high throughput sequencing.
Early Amniotic Membrane Transplantation in Bacterial Keratitis
ClinicalTrials.gov study NCT02716883. IPD Sharing: NO. Countries: 0. Publications: 0.
The polyaminoisoprenyl compound NV716 re-sensitizes antibiotics against Pseudomonas aeruginosa by perturbing outer membrane permeability and reduces bacterial virulence.
GEO Series GSE190194. Pseudomonas aeruginosa. 11 samples. Type: Expression profiling by high throughput sequencing.
Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles
GEO Series GSE102923. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Bacterial Elimination via Cell Membrane Penetration by Violet Phosphorene Peripheral Sub-Nanoneedles Combined with Oxidative Stress
GEO Series GSE226031. Escherichia coli. 6 samples. Type: Expression profiling by high throughput sequencing.
CAT-BF-SAAP-148-Fr_bacterial-membrane-liposomes_order-parameter_ssNMR_UNISTRA_2023-03-08
<p>Cathelicidin-BF, SAAP-148 and Frenatin 2.1s 2H ss NMR data of chain deuterated lipids POPE/POPG 3/1</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.