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266
datasets available to search
ShareScore release 0.9.0
Dataset results
266 results for “Protein Modelling”
Identification of early neurodegenerative changes in an induced pluripotent stem cell model of frontotemporal dementia linked to mutant tau protein
GEO Series GSE62935. Homo sapiens. 28 samples. Type: Expression profiling by array.
Heat Shock Proteins and Small Nucleolar RNAs are Dysregulated in a Drosophila Model for Feline Hypertrophic Cardiomyopathy
GEO Series GSE141574. Drosophila melanogaster. 40 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations
GEO Series GSE174182. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases I
GEO Series GSE236998. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
In vitro cell-line model to evaluate oncogenic functions associated with the HOXB13 protein with X285K variant
GEO Series GSE240364. Homo sapiens. 44 samples. Type: Expression profiling by high throughput sequencing.
Modeling of aniridia-related keratopathy by CRISPR/Cas9 genome editing of human limbal epithelial cells and rescue by recombinant PAX6 protein
GEO Series GSE139221. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins (ETS1 and RUNX1)
GEO Series GSE171734. Homo sapiens; synthetic construct. 4 samples. Type: Other.
Isogenic human pluripotent stem cell disease models reveal actin binding Rho activating protein deficiency underlies the cardiac troponin T DK210 mutation-induced familial dilated cardiomyopathy I
GEO Series GSE154096. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic profile of three-dimensional tissue-engineered human skeletal muscle model of Pompe disease and recombinant protein therapy
GEO Series GSE159062. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo 5dpf
GEO Series GSE295203. Danio rerio. 24 samples. Type: Expression profiling by high throughput sequencing.
Data from: Modelling dynamics in protein crystal structures by ensemble refinement
Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a 'molten core' likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships.
Protein Condensate Atlas from predictive models of heteromolecular condensate composition
Open the record for dataset details and reuse information.
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
<p>Data and checkpoints for 'Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models'</p>
Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"
<p><strong>Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models “Encode” Protein Folding and Protein-Protein Interactions"</strong></p> <p>This supplement includes the following files:</p> <ul> <li>Main_v02.R --- Script in R language to process protein structures and produce the datasets.</li> <li>datasets_v02.zip --- final filtered version of datasets produced in R language (by "Main_v02.R"). </li> <li>Dataset key v02.txt --- key and descriptions to column names in ("datasets.zip"). </li> </ul> <p>The article featuring these datasets is submitted to:</p> <p>Journal: Computers in Biology and Medicine (Reference: CBM_110033)<br>Title: "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"<br>Authors: Hameduh, Tareq; Miller, Andrew D. ; Heger, Zbynek; Haddad, Yazan</p> <p> </p> <p> </p>
Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling
<p><span>This dataset and accompanying R code support the manuscript titled "Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling," submitted to the Journal of Chemical Information and Modeling. The dataset primarily contains tables detailing the various chemicals, dependent, and independent variables used to develop two-parameter linear models for predicting muscle protein-water and serum albumin-water partition coefficients in this study. Additionally, it includes information on both observed and predicted values of these partition coefficients by newly developed models. The R code comprises scripts used for generating figures and results presented in the manuscript.</span></p> <p><span>The R code comprises scripts used for generating figures and results presented in the manuscript.</span></p> <p><span>These files are currently under restricted access for peer review purposes and will be made publicly available upon acceptance of the manuscript.</span></p>
Anabolic Potential of 3-hydroxybutyrate (3-OHB) and Whey Protein in a Human Catabolic Inflammatory Disease Model
ClinicalTrials.gov study NCT04064268. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Effect of HIV Tat Protein on HCV Replication in an In-vitro Model System
ClinicalTrials.gov study NCT01206933. IPD Sharing: NO. Countries: 1. Publications: 0.
Protein Sorbent Properties of Montmorillonite in Vitro and in Vivo Models
ClinicalTrials.gov study NCT02124330. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Upregulation of extracellular proteins in a mouse model of Alzheimer’s Disease
GEO Series GSE223417. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Systems modeling of oncogenic G-protein and oncogenic GPCR signaling reveals unexpected differences in downstream signaling pathway activation [CY_GQ_experiment]
GEO Series GSE267152. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.