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.
121
datasets available to search
ShareScore release 0.9.0
Dataset results
121 results for “crystal structure”
Data and scripts from "Unsupervised learning for structure detection in plastically deformed crystals"
<p>This documents contains the scripts and dataset used for the paper "Unsupervised learning for structure detection in plastically deformed crystals".</p> <p> </p> <p>More precisely it contains 4 folders :</p> <p><br> DumpForFigures : subfolder containing the atomic positions in .dump format (see lammps documentation) used for the article figures.</p> <p>DumpForTraining : subfolder containing the atomic position in .dump format (see lammps documentation) used for training the autoencoder.</p> <p>ScriptsToDetectStructuresFromDump : subfolder containing the script sused to detect the substructures of the system by combining autoencoder and clustering methods. This folder contains a readme with the details of the contents.</p> <p>ScriptToGenerateDump : subfolder containing the scripts used to generate the atomic data with molecular dynamics. These data are then used to train the autoencoder. This folder contains a readme with the details of the contents.</p> <p>REQUIREMENTS :</p> <p> </p> <p>Lammps</p> <p>Python3 with packages :</p> <p>-numpy</p> <p>-matplotlib</p> <p>-pyscal</p> <p>-sci-kit learn</p> <p>-pytorch</p> <p>-glob</p> <p> </p> <p> </p> <p> </p>
Experimental and Simulation Data for "Hierarchical structure formation by crystal growth-front instabilities during ice templating" (2023) PNAS
<pre>Experimental and Simulation Data for: "Hierarchical structure formation by crystal growth-front instabilities during ice templating" by Kaiyang Yin, Kaihua Ji, Louise Strutzenberg Littles, Rohit Trivedi, Alain Karma, Ulrike G.K. Wegst (2023) PNAS, DOI: 10.1073/pnas.2210242120. </pre>
Crystal Structure Solution and High Temperature Thermal Expansions of NaZr2(PO4)3-type Materials
<p>The NaZr<sub>2</sub>P<sub>3</sub>O<sub>12 </sub>(NZP) family<sub> </sub>of materials have shown low and tailorable thermal expansion properties. This dataset includes SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, NaTi<sub>2</sub>P<sub>3</sub>O<sub>12</sub>, NaZr<sub>2</sub>P<sub>3</sub>O<sub>12</sub>, MgZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, and related solid solutions. These materials were synthesized using the organic-inorganic steric entrapment method. The samples were characterized with in-situ high-temperature x-ray diffraction at the Advanced Photon Source and National Synchrotron Light Source II from 25 to 1500 ℃. The average linear thermal expansion of SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> and CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> was between -1 x10<sup>-6</sup>/℃ and 6 x10<sup>-6</sup>/℃ from 25 to 1500 ℃. High temperature polymorphs of CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> and SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> were solved by Fourier difference mapping and Rietveld refinement. This polymorph is present above about 1250 ℃. This work measured thermal expansion coefficients to 1500 ℃ for all samples and investigated the differences in thermal expansion mechanisms between polymorphs and between compositions. </p>
Crystal structure of glucose isomerase from S. rubiginosus soaked with EDTA for 1min
<p>Data: Diffraction images of crystal structure of glucose isomerase soaked with EDTA for 1min</p> <p>Experimental method: X-ray crystallography.</p> <p>Data collection: 11C beamline, Pohang Accelerator Laboratory</p>
Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. Part I: Adaptive local approximate models
<p>The global search stage of Crystal Structure Prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II (Habgood, M., Sugden, I. J., Kazantsev, A. V., Adjiman, C. S. & Pantelides, C. C. (2015).<em> J Chem Theory Comput</em> <strong>11</strong>, 1957-1969) program is presented, where the most efficient use of computational effort is ensured via the use of adaptive Local Approximate Model (LAM) placement. The entire search space of relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimise the computational effort expended in high energy regions whilst maximising the accuracy in low energy regions. As the size, complexity, and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule XXVI from the sixth blind test (Reilly <em>et al.</em>, (2016).<em> Acta Cryst. B, accepted</em>.), which is challenging due its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. </p>
Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years ‘on the shelf’
<p>These are the raw diffraction images for crystals 1 and 2 underpinning PDBe code 5LXW.</p>
Data from: Compromise docking power evaluation of liganded crystal structures of Mpro SARS-CoV-2
<p>A set of 406 liganded SARS-CoV-2 M<sup>pro</sup> crystal structures originally downloaded from RCSB PBD database is provided. Ligand and protein files are processed and corrected for various types of structural errors and are provided in pdbqt and mol2 formats for immediate use in molecular docking programs AutoDock, AutoDock Vina, and PLANTS. Data are utilized in calculations of newly defined compromise docking power to monitor the performance of above-mentioned software. The provided dataset can also be used for benchmarking of other software and molecular docking protocols on liganded SARS-CoV-2 M<sup>pro</sup> systems.</p>
Data for: Melt electrowriting enabled 3D liquid crystal elastomer structures for cross-scale actuators and temperature field sensors
<p>Liquid crystal elastomers have garnered significant attention due to their remarkable capability to undergo reversible strains and shape transformations under various stimuli. Early studies on LCE primarily focused on limited shape changes of macrostructures or quasi-3D microstructures. However, fabricating complex cross-scale LCE-based 3D structures still remains challenging. Here, we report a compatible method, the Melt-Electrohydrodynamic (Melt-EHD) 3D printing, to create LCE-based microfiber actuators and various 3D actuators across micrometer to centimeter scales, showcasing their actuation to thermal airflow stimulus. By controlling printing parameters, microfiber actuators with different diameters (5 μm~70 μm), and tunable properties including actuation strain (10%~55%), actuation stress (0~0.6 MPa), and large work density (~160J/kg) have been demonstrated. Under dynamic thermal airflow stimulus at 15 Hz, the microfiber actuators lift weights over 3500 times heavier than themselves. These 3D structures were obtained by depositing LCE microfibers along pre-programmed paths, including various gradient-responsive elementary structural units, 1 mm-sized microgripper, and various large area 3D lattice structures. In addition, by integrating a Deep Learning model, we have demonstrated, for the first time, large area (≥ centimeter scale), real-time (24 Hz sampling frequency), high-precision (~95%) LCE grid based spatial temperature field sensors with a spatial resolution of only 4 mm.</p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - 3lambda SeMAD dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) for 3 wavelength Se MAD experiment (infl, inflection point, peak, peak, rem, high energy remote) and the associated data processing files (xds_inf, xds_peak, xds_rem) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with an adenosine nucleotide analog.
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - native dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Curated data-set of crystal-structure prototypes of binary and ternary sp-d valent compounds
<p>Curated collection of binary and ternary compounds of sp-valent elements and d-valent elements and their crystal-structure prototype. The data set includes binary and pseudo-binary compounds in binary prototypes (BinaryPrototype-BinaryCompound.csv), offstoichoimetric and ternary compounds in binary prototypes (BinaryPrototype-BinaryOffstoichiometricAndTernaryCompound.csv) and ternary compounds in ternary prototypes (TernaryPrototype-TernaryCompound.csv). The first column in each data set corresponds to the crystal-structure prototype, the second column to the chemical composition. Ternary compositions labelled A-B+C indicate that element B and element C occupy the same sublattice of the crystal structure. A+B-C correspondingly indicates that element A and element B occupy the same sublattice. These data sets were used to construct structure maps for predicting the crystal structure of a compound from only its chemical composition. For details on curation, further discussions and structure maps see original publications (Chem. Mater. 28, 2550−2556, 2016 and Modelling Simul. Mater. Sci. Eng. 25, 074002, 2017).</p>
Crystal structure of natural product Argyrin-D determined by 3D electron diffraction
<p>360° rotation of the Argyrin D model (stick mode with carbon, yellow; nitrogen, blue; oxygen, red; sulfur, gold and hydrogen, white) defined by a 2Fo-Fc map contoured at 1.2 sigma (grey mesh). The model was refined at a resolution of 1.1Å in Phenix using implemented electron scattering factors and restraints to R and Rfree values of 17.3 and 18.6%, respectively.</p>
Original data for publications: Synthesis, Characterization, and Crystal Structures of Two New Manganese Aceto EMIM Ionic Compounds with Chains of Mn2+ Ions Coordinated Exclusively by Acetate, and: Fe4(OAc)10[EMIM]2: Novel Iron-Based Acetate EMIM Ionic Compound
<p>Origianl data for publications (Part of University of Geneva only):</p> <p>Synthesis, Characterization, and Crystal Structures of Two New Manganese Aceto EMIM Ionic Compounds with Chains of Mn2+ Ions Coordinated Exclusively by Acetate<br> Przemyslaw Dera, Edward Bruffey III, Gregory J. Finkelstein, Colleen Kelly, Angelina Gigante, Hans Hagemann, and Godwin Severa<br> ACS Omega 2020, 5, 25, 15592-15600</p> <p>Fe4(OAc)10[EMIM]2: Novel Iron-Based Acetate EMIM Ionic Compound<br> Godwin Severa, Edward Bruffey, Phuong Q. H. Nguyen, Angelina Gigante, Noemi Leick, Colleen Kelly, Gregory J. Finkelstein, Hans Hagemann, Thomas Gennett, Richard E. Rocheleau, and Przemyslaw Dera,<br> ACS Omega 2021, 6, 31907-31918.</p> <p> </p> <p> </p>
Co-crystal structures of USP5 Zf-UBD and weak binding compounds
<p>Determination of crystallization conditions which allow growth of well-diffracting co-crystals of USP5 zinc finger ubiquitin binding domain (Zf-UBD) and compounds shown to bind weakly by <a href="https://zenodo.org/record/1283325#.Wz5VXtJKjIV">19F NMR</a> and <a href="https://zenodo.org/record/1311686#.W0il_tJKjIU">SPR assays</a> & to solve the co-crystal structures to determine if electron density of ligands can be seen in the binding pocket of the protein domain.</p>
Crystal structure of olive flounder [Paralichthys olivaceus] interferon gamma at 2.3 Angstrom resolution - diffraction data
<p>Diffraction images, Bessy II (Berlin), MX 14.1, 12.5.2017, PDB ID 6F1E</p>
Robust and efficient reranking in crystal structure prediction: a data driven method for real-life molecules
<p>The content of this repository accompanies the publication "Robust and efficient reranking in crystal structure prediction: a data driven method for real-life molecules" and contains the complete dataset produced for the fentanyl CSP. </p> <p>Three types of datasets are present : Generation, ML-Reranker and GRACE. <br>Generation refers to all the molecular crystal structures that GRACE has generated using the tailor made force field. It's the starting pool of the reranking exercise, and it contains all the structures that will be selected by the reranking processes.<br>ML-Reranker refers to the data generated by the algorithm proposed in our manuscript. The configurations and energies are obtained by selecting from structures from the generation pool and relaxing their coordinates.<br>GRACE dataset contains the configurations which a user obtains at the end of a standard GRACE reranking procedure. Since GRACE follows differet convergence and minimization critera, the structures obtained in this dataset can differ (non-substantially) from the equivalents found in the ML-Reranker. </p> <p>*.data : contains the indices, energy of the crystal structure (kcal/mol) and, in case of the ml-reranker dataset, the indices mapping the obtained landscape to their generating pool.</p> <p>*.xyz : contains ASE formatted, extended-xyz list of structures corresponding to each exercise.</p> <p>Authors:</p> <p>Andrea Anelli, Hanno Dietrich, Philipp Ectors, Frank Stowasser, Tristan Bereau, Marcus Neumann, Joost van den Ende</p>
X-ray diffraction data on the crystal structures of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum
<p>X-ray diffraction data of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum</p> <p>Data type: raw data<br>Data format: cbf</p> <p>Data <br>1. TsaBgl-Tris Data I <br>2. TsaBgl-Tris Data II<br>3. TsaBgl-Tris Data III </p>
Associated coordinate and mtz files for "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides"
<p>Coordinate and mtz files for the associated protein structures reported in "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides".</p>
Atomic Structure of Amyloid Crystals
<p>3D ED/MicroED data collected on micro-crystals of a fragment of amyloid-beta peptide. The specimen was prepared using the Preassis method (Zhao et. al. Nature Communications 2021) on Quantifoil R2/1 (300 mesh) grid. 3D ED/MicroED data were collected on a 200kV JEOL JEM-2100 LaB<sub>6 </sub>TEM equipped with a Timepix hybrid pixel detector. A Gatan 914 cryo-transfer holder was used to keep the specimen at liquid nitrogen temperature during data collection. The rotation speed of goniometer, exposure time, electron dose rate and camera length were 0.23 degree/s, 0.5 s, 0.1 e<sup>-</sup>/Å<sup>2</sup>/s and 30cm, respectively. The software <em>Instamatic </em>was used for electron diffraction data collection. The rotation range of individual dataset was limited between 40 degree and 50 degree due to beam damage.</p> <p>The data was saved in TIFF, SMV, and DM3 (for REDp processing) format. Information of the individual data collection can be found in the cRED_log file. Input files for PETS processing and XDS processing (automatically generated) are also included.</p> <p> </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.