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3,655 results for “Structural data”
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Data from: The evolution of protein-coding gene structure in eukaryotes
<p>Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here we explore the evolution of the eukaryotic gene intron-exon structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon ratio of protein-coding genes. We utilize whole genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic phyla, with animals, and particularly chordates, displaying intron-rich genes, compared to plants and fungi. Reconstruction of gene structure evolution suggests that these differences had evolved prior to the divergence of the phyla, and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length, and report that the correlation patterns differ considerably among phyla. Our findings suggest that the evolution of introns may be affected by different processes across the eukaryotic tree. The substantial diversity in gene structures may indicate that introns play different molecular and evolutionary roles in different organisms.</p>
Convergence in simulating global soil organic carbon by structurally different models after data assimilation
<p>This is the data for results shown in the article accepted by Global Change Biology: Convergence in simulating global soil organic carbon by structurally different models after data assimilation</p>
Raw data for: Structural and mechanistic insights into human choline and ethanolamine transport
This repository contains raw data related to "Structural and mechanistic insights into human choline and ethanolamine transport" by Ri et al. <div> <p>Included are molecular dynamics parameter files, initial structures after system equilibration and production trajectories. Trajectories are subsampled with one frame every 10 ns. <br><br></p> <p>Contact information:</p> <p><br>Name: Ainara Claveras Cabezudo<br>Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br>Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br>Email: ainara.claveras@biophys.mpg.de</p> </div>
Simulation Data for Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination
<p>This is supporting information for an upcoming research manuscript. The uploaded tarball contains the directory structure needed to reproduce the simulations conducted to support the forthcoming article. The directory structure has three primary subdirectories, Alphafold which contains the initial structure predictions, Build, which has the Tcl scripts in VMD to assemble the system, and Simulation, which has the simulations themselves and the analysis. Since there is a limit to the file sizes that can be stored on Zenodo, we exclude many files to fit under the limit. The command to create the tarball was: <code>tar --exclude=LukeSim --exclude="*trr" --exclude="*dcd" --exclude="*GO*" --exclude="*HPR*" --exclude="*PGP*" --exclude="*GAT*" --exclude="*#" --exclude="*ppm" --exclude="*BAK" --exclude="*oldpgp*" -zcvf glykthermostable.tar.gz Thermostability/</code></p> <p>While the full trajectories are too large to be provided, reduced trajectories of only the protein component can be found in the <code>Thermostability/Simulation/Analysis/prottrajs</code> path. Files with the <code>.js</code> extension can be read via VMD.</p>
Fig. 3 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 3. Likelihood phylogeny of concatenated supermatrix of Pogonolepis and outgroups. Numbers above branches indicate UltraFast Bootstrap values, gene Concordance Factors, and site Concordance Factors. The dashed branch was shortened for the figure. Western Australian specimens of P. muelleriana are marked with (WA), all others are from eastern states. A and B indicate informally named clades inside P. stricta.
Fig. 2 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 2. Geographic spread of the specimens of Pogonolepis at CANB sampled for molecular analysis (large, pale circles) and ranges of species according to the Australasian Virtual Herbarium (dots; see https://doi.org/10.26197/ala.6556e234- 7160-49de-bf63-5123af624e94, accessed 31 May 2022). Red: P. muelleriana; blue: P. stricta. Note that specimens of P. muel-leriana geocoded in Canberra and Hobart were likely cultivated.
Fig. 1 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 1. (a) Pogonolepis muelleriana, New South Wales, SchmidtLebuhn 1633 (CANB); (b) Pogonolepis stricta, Western Australia, Schmidt-Lebuhn 1474 (CANB).
Supporting data for "A method for non-linear inversion of the stellar structure applied to gravity-mode pulsators"
<p>These are the inlist and run_star_extras required to reproduce the stellar and asteroseismic models presented in 'A method for non-linear inversion of the stellar structure applied to gravity-mode pulsators', run with MESA r22.05.1.</p>
Data Sets For: Heterogeneous Structure, Mechanisms of Counterion Exchange, and the Spacer Salt Effect in Complex Molten Salt Mixtures Including LaCl3
<p>Data Sets For: Heterogeneous Structure, Mechanisms of Counterion Exchange, and the Spacer Salt Effect in Complex Molten Salt Mixtures Including LaCl3</p>
Data from: Plasticity and the structural characteristics of personality traits in captive-reared Japanese quail during ontogeny
<p>This dataset contains the measurements of different personality traits in a study on Japanese quail.</p>
Simulation Input Data for "Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics"
<p>This is the reduced data behind an upcoming manuscript investigating impact of acetylation on plant secondary cell wall. 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> <p> </p> <pre><code>tar -zcvf Acetylatedcellwall.tar.gz --exclude="*BAK" --exclude="*dcd" --exclude="*poster*" --exclude="*old" --exclude="*out" --exclude="*vel" --exclude="*ppm" --exclude="*mp4" --exclude="*txt" --exclude="*tga" --exclude="*vmd" --exclude="*log" --exclude="fixed*png" --exclude="frame*png" --exclude="nonacetylation*png" . </code></pre>
Dataset: Chromatographic data for publication Exploration and optimisation of structure-activity relationships of newtriazole-based C-terminal Hsp90 inhibitors towards in vivoanticancer potency
<p>Bio-chromoatographic data caming from publication Exploration and optimisation of structure-activity relationships of new triazole-based C-terminal Hsp90 inhibitors towards in vivo anticancer potency</p>
Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure Data and Code
<p>This dataset includes all data used for the creation of "Including dynamic population and environmental heterogeneity in continuum models of collective behaviour with applications to locust foraging and group structure" as well as a snapshot of the code used.<br><br>Each zip should be unzippable and the code should operate with only the contents of the zip file.</p>
Data Set from Quasi-static Cyclic Tests of Scoured 2×3 Pile-Group Foundations for Bridge Structures
<p>This data set is from Quasi-static cyclic tests of scoured 2×3 pile-group foundations for bridge structures, as a data paper submitted to Earthquake Spectra (Submission ID: EQS-24-0190)</p>
Data set of Magnetic stability of magnetite particles with single vortex structure during low temperature oxidation
<p>Data set of Magnetic stability of magnetite particles with single vortex structure during low temperature oxidation</p>
Data from: Fractal characteristics of shale pore structure and its influence on seepage flow
<p>The migration law of shale gas has a significant influence on the seepage characteristics of shale, and the flow of the gas is closely related to the pore structure. To explore the influence of shale pore parameters on permeability in different diffusion zones, the pore structure of the shale in the Niutitang Formation in Guizhou, China, was analyzed based on liquid nitrogen adsorption experiments and nuclear magnetic resonance experiments. The relationship among fractal dimension, organic carbon content (TOC), and BET specific surface area was analyzed based on the fractal dimension of shale pores calculated using the Frenkel‒Halsey‒Hill model. Shale permeability was calculated using the Knudsen number and permeability equation, and the influence of the fractal dimension and porosity in different diffusion zones on shale permeability was analyzed. Previous studies have shown that: (1) the pores of shale in the Niutitang Formation, Guizhou are mainly distributed within 1‒100 nm, with a small total pore volume per unit mass, average pore diameter, large BET specific surface area, and porosity; (2) fractal dimension has a negative correlation with average pore diameter and TOC content and a quadratic relationship with BET specific surface area; (3) permeability has a positive correlation with Kn, porosity, and fractal dimension. In the transitional diffusion zone, fractal dimension and porosity have a significant impact on permeability. In the Knudsen diffusion zone, porosity has no obvious effect on permeability. The methodologies and results presented will enable more accurate characterization of the complexity of pore structures of porous media, and allow further understanding of the seepage law of shale gas.</p>
Data set (stata format) + do file for : Risk misperceptions of structured financial products with worst-of payout characteristics revisited
<p>This file contains the data set (in stata format) and do file associated with the paper entitled "Risk misperceptions of structured financial products with worst-of payout characteristics revisited"</p>
Data for "Association of lightning occurrence with precipitation cloud column structure at a fixed position"
<p>Here are the data for the paper titled "Association of lightning occurrence with precipitation cloud column structure at a fixed position" and submitted to Atmospheric Research. The abstract is as follow.</p> <p> </p> <p>In this study, a C-band frequency-modulated continuous-wave (C-FMCW) radar, with its feature of vertical detection, was combined with lightning discharge recordings within a 3 km range to investigate the dependence of lightning occurrence on the structure of precipitation cloud columns (PCCs) from the perspective of a fixed position. The results show that, relative to PCCs without lightning, PCCs with lightning exhibit greater maximum reflectivity, maximum upward radial velocity, maximum velocity spectrum width, cloud top height, and vertically integrated liquid in terms of their average values, and wider-range distributions of these parameters. Using the Light Gradient Boosting Machine algorithm, a lightning diagnosis program that integrates multiple C-FMCW radar parameters was developed. Its hit rate of lightning occurrence is 93.5% and it has a threat score of 0.421. The maximum velocity spectrum width above the melting layer was found to be the most effective in distinguishing PCCs with or without lightning. It was suggested that the hydrometeor properties at a specific location, specifically the size diversity and content of ice-phase particles, should be the key elements determining the occurrence of lightning discharge in PCCs; meanwhile, the convection characteristics in the PCCs may be not the most critical.</p>
Data, Codes for 'Electronic Structure and Epitaxy of CdTe Shells on InSb Nanowires'
<p>Measurement_Raw_data.zip:</p> <p> Full Original Raw Data for all devices.</p> <p>Measurement summary.zip:<br> Measurement and fit method summary (in PPT).</p> <p>Simulation and Fit.zip:<br> Code for capacitance simulation and data fitting.</p> <p>Measurement Log.zip:</p> <p> Word file contain all commends used in measurement and correspond results.<br> </p> <p>Data formats:<br> MTX:<br> A simple 2D/3D matrix format developed for Spyview (https://nsweb.tn.tudelft.nl/~gsteele/spyview/).</p> <p> DAT:<br> Original plain-text tabular data.</p> <p> SET:<br> Instrument settings.</p> <p> PY:<br> Measurement scripts.</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.