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144 results for “Protein stability”
Overcoming Limitation of AlphaFold2 by Deep-mutational Scanning and Stability-Selection of Protein Sequences
<p>This repository contains the processed datasets and corresponding code used in our study. While AlphaFold2 revolutionizes protein structure prediction, its accuracy critically depends on evolutionary information from natural homologs—limiting applications for proteins with sparse sequence families. Here, we bypass this bottleneck by employing deep mutational scanning and stability-guided selection to generate artificial homologs. Fed into AlphaFold2, these synthetic sequences match the accuracy achieved on well-predicted proteins with rich natural homology, while providing highly accurate predictions for difficult targets—including orphan proteins previously deemed "unpredictable." Our approach achieves high accuracy (<3 Å RMSD for 5/8 and <2 Å RMSD for 7/8 targets after excluding intrinsically flexible regions). Thus, integrating simple, scalable molecular biology (mutagenesis/selection) with high-throughput sequencing can deliver the accuracy similar to but at a fraction of the cost and time of traditional experimental structure-determination methods. This hybrid framework could democratize high-resolution structural biology, opening avenues to determine structures of protein complexes, modified proteins, and condition-dependent conformations. </p>
Stability Increase of Phenolic Acid Decarboxylase by a Combination of Protein and Solvent Engineering Unlocks Applications at Elevated Temperatures
<p>Enzymatic decarboxylation of biobased hydroxycinnamic acids gives access to phenolic styrenes for adhesive production. Phenolic acid decarboxylases are proficient enzymes that have been applied in aqueous systems, organic solvents, biphasic systems, and deep eutectic solvents, which makes stability a key feature. Stabilization of the enzyme would increase the total turnover number and thus reduce the energy consumption and waste accumulation associated with biocatalyst production. In this study, we used ancestral sequence reconstruction to generate thermostable decarboxylases. Investigation of a set of 16 ancestors resulted in the identification of a variant with an unfolding temperature of 78.1 °C and a half-life time of 45 h at 60 °C. Crystal structures were determined for three selected ancestors. Structural attributes were calculated to fit different regression models for predicting the thermal stability of variants that have not yet been experimentally explored. The models rely on hydrophobic clusters, salt bridges, hydrogen bonds, and surface properties and can identify more stable proteins out of a pool of candidates. Further stabilization was achieved by the application of mixtures of natural deep eutectic solvents and buffers. Our approach is a straightforward option for enhancing the industrial application of the decarboxylation process.</p>
Data for Stabilization of non-native folds and programmable protein gelation in compositionally designed deep eutectic solvents
<div> <p>Full set of data related to the publication "Stabilization of non-native folds and programmable protein gelation in compositionally designed deep eutectic solvents", published in ACS Nano with DOI:<a title="https://doi.org/10.1021/acsnano.4c01950" href="https://doi.org/10.1021/acsnano.4c01950">10.1021/acsnano.4c01950</a></p> <p> Full details on data treatment and logging are included in the file "DataLogging.pdf". All data use ASCII encoding in delimited .txt files.</p> <p> </p> </div>
DATASET: Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona
<p>This dataset contains the DLS, CD, fluorescence, ITC, TEM, and ANS raw data used for the manuscript.</p>
Data for Hydration in Deep Eutectic Solvents Induces Non-monotonic Changes in the Conformation and Stability of Proteins
<p>This dataset contains the full set of data related to the publication "Hydration in Deep Eutectic Solvents Induces Non-monotonic Changes in the Conformation and Stability of Proteins", published in the Journal of the American Chemical Society 2022, 144 (51), 23657-23667; doi: 10.1021/jacs.2c11190. Full details on data treatment and logging are included in the file "DataLogging.pdf". All data use ASCII encoding in delimited .txt files.</p>
FireProtDB + PDB Structural Protein Stability Dataset
<p>Dataset compiled and curated for use in the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>: </p> <p>Dataset for training models for prediction of thermodynamic stability changes (ddG) of protein point mutations given a wildtype protein structure (PDB) file. Data was assembled by matching sequence-based ddG measurements in <a href="https://loschmidt.chemi.muni.cz/fireprotdb/">FireProtDB</a> to structures from the <a href="https://www.rcsb.org/">RCSB Protein Data Bank </a>(PDB). For details, see the Methods section of our manuscript.</p> <p>Citing this work: If you choose to use this dataset for your own research, please cite this repository and the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>.</p> <p> </p> <p>Contents:</p> <p>pdbs/ directory contains all PDB files</p> <p>csvs/ directory contains all CSVs with mutation data</p> <p>csvs/4_fireprotDB_bestpH.csv is the main (full) dataset file with 3,438 mutations across 100 proteins.</p> <p>csvs/fireprot_splits.pkl contains the dataset splits (train/val/test) used in our study</p> <p>csvs/splits/ contains csvs for each of the splits (train/val/test/homologue-free) indexed from the full dataset csv.</p> <p>Important CSV columns:</p> <ul> <li>pdb_id_corrected: corresponds to the PDB in the pdbs/ directory (after curation and disambiguation)</li> <li>ddG: ddG value for mutation (mutant - WT)</li> <li>wild_type: wild-type amino acid (1-letter code)</li> <li>mutation: mutant amino acid (1-letter code)</li> <li>pdb_position: 0-based index of the mutated residue in the PDB file (may be different from position in the original FireProtDB sequence entry)</li> </ul> <p> </p>
The prefoldin complex stabilizes the von Hippel-Lindau protein against aggregation and degradation
<p>This is the dataset corresponding to our submitted article "The prefoldin complex stabilizes the von Hippel-Lindau protein against aggregation and degradation" by Chesnel et al.</p>
Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin
<p>Pharmacological activation of hypoxia-inducible factor 1alpha (HIF-1α), a hypoxia-responsive transcription factor, has attracted increasing attention due to its efficacy not only in renal anemia but also in various disease models. Our study demonstrated that a HIF-1 activator enhanced exosome production from cultured endothelial cells synergistically with adiponectin, an adipocyte-derived factor, through both transcriptional induction and posttranscriptional stabilization of an adiponectin binding partner, T-cadherin. Increased exosome levels were observed in wild-type mice but not in T-cadherin null mice after consecutive administration of roxadustat. Adiponectin- and T-cadherin-dependent increased exosome production may be involved in the pleiotropic effects of HIF-1 activators.</p>
Insights into the stability of engineered mini-proteins from their dynamic electronic properties
<p>Coordinates and partial charges from GFN2-xTB and wPBEh/cc-pvdz for 20 ps x 20 replicas for two variants of Trp-cage (TC5b and TC10b) as supporting information.</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>
Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor SlCYS8 in Nicotiana benthamiana
<p>Complete dataset (MS Label-free quantification) for the publication 'Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor <em>Sl</em>CYS8 in <em>Nicotiana benthamiana</em>'</p> <p>DOI: 10.1111/pbi.13092</p> <p> </p>
Thermodynamics-driven, high-throughput analysis of protein stability with MoltenProt
<p>Data for thermal unfolding curves for various proteins.</p> <p>Measured parameters: intrinsic fluorescence (330nm, 350nm), scattering</p> <p>Files in XLSX format represent annotated output data from NanoTemper Prometheus NT.48.</p> <p> </p>
Data accompanying "In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers" article.
<p>This research was supported by the National Science Centre, Poland, grant PRELUDIUM number 2021/41/N/NZ1/03473 to NS, National Science Centre, Poland, grant SONATA BIS number 2019/34/E/NZ6/00354 to DG-O, as well as POIR.04.04.00-00-21FA/16–00 grant, carried out within the First TEAM programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (awarded to DG-O). WP was supported by the National Science Centre, Poland, grant SONATA-BIS number 2021/42/E/NZ1/00190. SB is supported by a Wellcome Trust Senior Research Fellowship (220875/Z/20/Z).</p>
A Study of an Adenovirus Serotype 26 Pre-fusion Conformation-stabilized F Protein (Ad26. RSV. preF) Based Respiratory Syncytial Virus (RSV) Vaccine in the Prevention of Lower Respiratory Tract Disease
ClinicalTrials.gov study NCT04908683. IPD Sharing: YES. Countries: 14. Publications: 1.
Dose, Safety, Tolerability and Immunogenicity of a Stabilized Prefusion RSV F Subunit Protein Vaccine, VRC-RSVRGP084-00-VP (DS-Cav1), Alone or With Alum Adjuvant, in Healthy Adults
ClinicalTrials.gov study NCT03049488. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin
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An amphipol-stabilized multi-pass transmembrane protein as an immunogen to generate mouse memory B cells against native VMAT2
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A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
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Unraveling the Unfolding Mechanism of Pseudoazurin: Insights into Stabilizing Cupredoxin Fold as a Common Domain of Cu-Containing Proteins
<p>This dataset includes molecular dynamics (MD) simulation trajectories and experimental data used in the title named study. The MD trajectories cover simulations of pseudoazurin under various conditions: apo (pH 2, pH 3, pH 7), holo (pH 2, pH 3, pH 7), and explicit water simulations of holo at pH 7. Additionally, the dataset contains raw experimental data, including small-angle neutron scattering (SANS) curves, visible (Vis) absorption spectra, and circular dichroism (CD) spectra. This comprehensive dataset supports the investigation of unfolding mechanism of Pseudoazurin.</p>
Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized Emulsions: Yield Stress Decay and Protein Release
<p>Raw data for our publication "Non-Invasive Rheo-MRI Study of Egg Yolk-Stabilized Emulsions: Yield Stress Decay and Protein Release", including MRI (Paravision) and D-T2 maps (Topspin) datasets, rheological measurements (ASCII) and MATLAB scripts organised corresponding to each figure in the paper.</p>
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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.
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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.