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347
datasets available to search
ShareScore release 0.9.0
Dataset results
347 results for “structural proteins”
Global signatures of protein binding on structural RNAs in Saccharomyces cerevisiae
GEO Series GSE48888. Saccharomyces cerevisiae. 10 samples. Type: Expression profiling by high throughput sequencing.
The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus
GEO Series GSE41154. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [RNA-seq]
GEO Series GSE200691. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly
GEO Series GSE186409. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
GEO Series GSE58974. Arabidopsis thaliana. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Constitutive stringent response restores viability of Bacillus subtilis lacking Structural Maintenance of Chromosome protein
GEO Series GSE73315. Bacillus subtilis subsp. subtilis str. 168. 7 samples. Type: Expression profiling by array.
Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins
GEO Series GSE107301. Escherichia coli str. K-12 substr. MG1655. 35 samples. Type: Expression profiling by high throughput sequencing; Other.
Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis
GEO Series GSE142242. Mus musculus. 24 samples. Type: Other.
Human Respiratory Syncytial Virus Non-Structural Protein NS1 enters the nucleus to disrupt gene transcription
GEO Series GSE155152. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
L3MBTL2 protein acts in concert with PcG protein mediated monoubiquitination of H2A to establish a repressive chromatin structure [ChIP-Seq data].
GEO Series GSE28162. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
L3MBTL2 protein acts in concert with PcG protein mediated monoubiquitination of H2A to establish a repressive chromatin structure [ChIP-chip data].
GEO Series GSE28161. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment
GEO Series GSE200673. Mus musculus. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other.
Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing
GEO Series GSE121713. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Gene structure, differential exon usage, and expression of the testis long intergenic non-protein coding RNA 1016 in humans reveals isoform-specific roles in controlling biological processes
GEO Series GSE171047. Homo sapiens. 16 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.
Structure prediction of protein-ligand complexes from sequence information with Umol
<p>posebusters_benchmark_set.tar.zst - files for the prediction (features to Umol) and scoring of the pose busters benchmark </p><p>posebusters_pred_native.tar.zst - pdb and sdf files of proteins and ligands. Includes native structures, predicted structures and relaxed predicted structures with plDDT in the B factor column.</p><p>posebusters_scores.csv - contains ligand RMSD and other metrics for the unrelaxed structures predicted with Umol.</p><p>PDBBind_processed.tar.zst - files for the training (features to Umol) using PDBbind version 2020</p><p> </p><p> </p>
Reseek protein structure databases
<p>Protein Data Bank (<a href="https://www.rcsb.org/">PDB home page</a>) snapshot from Nov 2nd 2024 in Reseek .bca format.<br><br>SCOP40 database in .bca format (<a href="https://scop.berkeley.edu/">SCOP home page</a>).<br><br>See home pages for licenses and references.</p>
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
<p>The COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.</p>
Dataset from: Structure-based prediction of protein-nucleic acid binding using graph neural networks
<p>Datasets used for training/evaluating the neural network models described in our article. Additional documentation related to how these datasets were constructed can be found in the github repository https://github.com/jaredsagendorf/pnabind/tree/master/datasets</p>
A joint embedding of protein sequence and structure enables robust variant effect predictions
<p>Data related to the GitHub repository KULL-Centre/_2023_Blaabjerg_SSEmb, which is also stored on Zenodo here: <span><span><a href="../doi/10.5281/zenodo.13765792" target="_blank" rel="noopener noreferrer">https://zenodo.org/doi/10.5281/zenodo.13765792</a>.</span></span></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.