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Dataset results
295 results for “Structure prediction”
AlphaFold_ab_initio iterative structure predictions sub trajs for faster download
<p>PDB ids start from 2 (61-118).</p> <div> <p>Check related biorxiv preprint: AlphaFold2 knows some protein folding principles; DOI: https://doi.org/10.1101/2024.08.25.609581.</p> <p> </p> </div>
AlphaFold_ab_initio iterative structure predictions sub trajs for faster download
<p>PDB ids start from 5 (1-73).</p> <div> <p>Check related biorxiv preprint: AlphaFold2 knows some protein folding principles; DOI: https://doi.org/10.1101/2024.08.25.609581.</p> <p> </p> </div>
Supporting dataset for "27Al NMR chemical shifts in zeolite MFI via machine learning acceleration of structure sampling and shift prediction"
<p>This dataset includes includes training databases of CHA, MOR and MFI zeolites, trained kernel ridge regression (KRR) models, and the initial structures utilized in the study. A more detailed description of the dataset can be found in the README file.</p> <p>Note, all MD simulations were performed using SiAlOH1 ML potential from the work of Erlebach et al. (Erlebach et al., Nat Commun 15, 4215 (2024)), available at: https://doi.org/10.5281/zenodo.10361794.</p>
DFT-predicted equilibrium structures and electron transfer coordinate: CuPYBCP, CoPYN5, and CuPYBCP-CoPYN5
<p>Fully relaxed equilibrium structures of <strong>CuPYBCP</strong>, <strong>CoPYN5</strong>, and <strong>CuPYBCP</strong>-<strong>CoPYN5</strong> as predicted at the DFT level of theory (PBE0/def2-SVP) including D3BJ dispersion correction and implicit solvent effects (acetonitrile). The total charge as well as the multiplicity are indicated in the filename of the respective structure, e.g., “CuPYBCP-1.1-FC.xyz” being the ground state structure of <strong>CuPYBCP</strong> with a charge of “1” and with a multiplicity of “1” (singlet), while “CuPYBCP-0.2-FC.xyz” is the structure of its singly reduced “0” (uncharged) doublet “2” ground state. In case of the triplet intermediates, the labels “IL” (intraligand) and “MLCT” (metal-to-ligand charge transfer) indicate the electronic nature of the respective open-shell species.</p> <p>Structures along the electron transfer coordinate (<em>R</em><sub>ET</sub>) in <strong>CuPYBCP-CoPYN5</strong>, approximated by means of a linear-interpolated internal coordinate (LIIC) that connects the equilibrium structure of the electron donor state “D” and electron acceptor state “A”, are summarized in one trajectory file “CuPYBCP-CoPYN5-LIIC-2.3.trj”.</p>
DFT and TDDFT-predicted equilibrium structures of bipyridine-annulated perylene tetracarboxylic ester photocatalysts with PdCl2 and PtCl2
<p>Fully relaxed equilibrium structures of <strong>P-Pd</strong> and <strong>P-Pt</strong> as predicted at the DFT and TDDFT levels of theory (B3LYP/def2-SVP) including D3BJ dispersion correction and implicit solvent effects (CH<sub>2</sub>Cl<sub>2</sub>). Both photocatalysts were optimized in singlet (S0) and triplet multiplicity in order to evaluate the Franck-Condon photophysics as well as the prominent triplet species involved in the photphysical and photochemical properties, i.e. triplet intra-ligand (3IL) and triplet metal-to-ligand charge transfer (MLCT) states. The multiplicity is indicated in the filename.</p>
Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction, 2014
<p>This contains the protein sequence and secondary structure dataset from <a href="https://proceedings.mlr.press/v32/zhou14.html"><strong>Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction</strong></a><strong>, ICML, 2014</strong></p> <p>This dataset was originally hosted at http://www.princeton.edu/~jzthree/datasets/ICML2014/. Since the original URL is no longer available and the dataset is still used by many, I moved the dataset here.</p>
LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules
<p>LinearCoFold and LinearCoPartition</p>
Supporting Material for manuscript "Structure Prediction of Ionic Epitaxial Interfaces with Ogre Demonstrated for Colloidal Heterostructures of Lead Halide Perovskites"
<p>This database contains the Supporting Material for the ChemrXiv preprint entitled "Fast Prediction of Ionic Epitaxial Interfaces with Ogre Demonstrated for Colloidal Heterostructures of Lead Halide Perovskites", authored by Stefano Toso, Derek Dardzinski, Liberato Manna and Noa Marom. The database contains:</p> <p>· Ogre simulations for all the epitaxial interfaces discussed in the manuscript, provided as raw output.</p> <p>· Installation wizards for the OgreInterface application (available for Windows, Linux, and Mac).</p> <p>· Jupyter Notebook interface to run the Ogre library with more flexibility.</p> <p>· Jupyter Notebook interface to reproduce all simulations discussed in the manuscript.</p> <p>· Reference CIFs for all the materials discussed in the manuscript.</p> <p>· VESTA atomistic models of all the interfaces discussed in the manuscript (Main Text only).</p>
Performance of Large Language Models for Structured Recognition and Refractive Prediction
ClinicalTrials.gov study NCT07183891. IPD Sharing: NO. Countries: 1. Publications: 0.
Tertiary Lymphoid Structures Related Genes Predicting Prognosis in Clear Cell Renal Cell Carcinoma: a Retrospective Cohort Study
ClinicalTrials.gov study NCT06883565. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Heterogeneity of Tertiary Lymphoid Structures Predicts Distinct Malignancy and Immune Microenvironment in Prostate Cancer: a Retrospective Cohort Study
ClinicalTrials.gov study NCT06484127. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Combined Whole-brain Structural and Functional MRI for the Prediction of Neurological Recovery After Cardiac Arrest
ClinicalTrials.gov study NCT06617377. IPD Sharing: NO. Countries: 0. Publications: 0.
Structuring of a Lung Cancer Screening Program Including Clinical, Radiological and Biological Phenotyping Useful for the Development of Individualized Risk Prediction Tools: PREVALUNG ETOILE
ClinicalTrials.gov study NCT05649046. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Efficient, Holistic, Heuristic and Semi-structured Suicide Assessment Tool (EHSSA) - Very Accurate Prediction of Risk.
ClinicalTrials.gov study NCT04888533. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
ChIP on chip "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"
GEO Series GSE5992. Toxoplasma gondii; Toxoplasma gondii RH. 14 samples. Type: Genome binding/occupancy profiling by genome tiling array.
An siRMSD parameter of structural distortion induced by chemical modification is predictive of the off-target effect of siRNA_(1/2)
GEO Series GSE278438. Homo sapiens. 7 samples. Type: Expression profiling by array.
Gene expression "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"
GEO Series GSE5989. Homo sapiens; Toxoplasma gondii; Toxoplasma gondii RH. 3 samples. Type: Expression profiling by array; Expression profiling by genome tiling array.
Data from: Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots
Open the record for dataset details and reuse information.
Data from: Near infrared spectroscopy (NIRS) predicts non-structural carbohydrate concentrations in different tissue types of a broad range of tree species
Open the record for dataset details and reuse information.
Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture (human)
GEO Series GSE92290. Homo sapiens. 4 samples. Type: Other.
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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.