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471 results for “Protein targets”
Targeting protein-ligand neosurfaces with a generalizable deep learning tool
<p>Molecular recognition events between proteins drive biological processes in living systems. However, higher levels of mechanistic regulation have emerged, where protein-protein interactions are conditioned to small molecules. Despite recent advances, computational tools for the design of novel chemically-induced protein interactions have remained a challenging task for the field. Here, we present a computational strategy for the design of proteins that target neosurfaces, i.e. surfaces arising from protein-ligand complexes. To do so, we leveraged a geometric deep learning approach based on learned molecular surface representations and experimentally validated binders against three drug-bound protein complexes: Bcl2:Venetoclax, DB3:Progesterone and PDF1:Actinonin. All binders demonstrated high affinities and accurate specificities assessed by mutational and structural characterization. Remarkably, surface fingerprints previously trained only on proteins can be applied to neosurfaces emerging from small molecules, serving as a powerful demonstration of generalizability that is uncommon in other deep learning approaches. We anticipate that the designed chemically-induced protein interactions hold the potential to expand the sensing repertoire and the assembly of new synthetic pathways in engineered cells for innovative drug-controlled cell-based therapies</p>
Trajectories from "A glutamine-based single ɑ-helix scaffold to target globular proteins" Escobedo et al. 2022
<p>Trajectories from the manuscript "A glutamine-based single ɑ-helix scaffold to target globular proteins" Escobedo et al. 2022.</p> <p>https://www.biorxiv.org/content/10.1101/2022.05.06.490931v1</p>
TIRF Microscopy Data Files. "Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides: Implications for target site search"
<p>TIRF-microscopy images and analysis data from single-molecule experiments assessing the direct transfer phenomenon in the TREX1 exonuclease. </p>
Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1
<p>Raw experimental data for the manuscript entitled 'Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1'. This includes the data underlying all figures, DESeq2 files, modeling and MD simulations, and chemical compound characterization (NMR, LC-MS, HRMS). Also, the custom Matlab script to analyse cilium intensity from microscopy images is included (cilia-track_v4.0).</p>
Cancer Vaccine Targeting Brachyury Protein in Tumors
ClinicalTrials.gov study NCT01519817. IPD Sharing: NO. Countries: 1. Publications: 5.
A Study Evaluating Targeted Therapies in Participants Who Have Advanced Solid Tumors With Genomic Alterations or Protein Expression Patterns Predictive of Response
ClinicalTrials.gov study NCT04632992. IPD Sharing: YES. Countries: 1. Publications: 1.
Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia
Open the record for dataset details and reuse information.
Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein
Open the record for dataset details and reuse information.
Hoi1 targets the yeast BLTP2 protein to ER-PM contact sites to regulate lipid homeostasis
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Data from: Development of folate receptor targeting chimeras for cancer selective degradation of extracellular proteins
Open the record for dataset details and reuse information.
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
<p>The Krogan Laboratory used affinity-purification mass spectrometry to identify 332 high confidence SARS-CoV-2-human protein-protein interactions, including 67 druggable human proteins or host factors targeted by 69 known drugs. Results may be relevant to antiviral drug production.</p>
Supplemental data: Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence
<p>This dataset supplements the chapter "Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence" published in Methods in Molecular Biology. It includes sample files that illustrate data collection and processing outlined in the article.</p>
Molecular dynamics trajectory videos for high-affinity short peptides targeting BamA protein of Candidatus liberibacter asiaticus
<p>Molecular dynamics trajectory videos and trajectory analysis reports for high-affinity short peptides targeting BamA protein of <em>Candidatus</em> liberibacter asiaticus</p>
Targeting host-virus interactions: In silico analysis of the binding of human milk oligosaccharides to viral proteins involved in respiratory infections
<p><span>Respiratory viral infections, a major public health concern, necessitate the continuous development of novel antiviral strategies, particularly in the face of emerging and re-emerging pathogens. In this study, we </span><span>explored</span><span> the potential of human milk oligosaccharides (HMOs) as broad-spectrum antiviral agents against key respiratory viruses. </span><span>By examining the</span><span> structural mimicry of host cell receptors and </span><span>their </span><span>known biological functions, including antiviral activities, we assessed the </span><span>ability</span><span> of HMOs to bind and potentially inhibit viral proteins crucial for host</span><span> </span><span>cell entry. Our <em>in silico</em> analysis </span><span>focused</span><span> on viral proteins integral to host-virus interactions</span><span>, namely,</span><span> the hemagglutinin protein of influenza, fusion proteins of respiratory syncytial and human metapneumovirus, and the spike protein of SARS-CoV-2. Using molecular docking and simulation studies, we </span><span>demonstrated</span><span> that HMOs exhibit varying binding affinities to these viral proteins, suggesting their potential as viral entry inhibitors. </span><span>This</span><span> study </span><span>identified</span><span> several HMOs with promising binding profiles, highlighting their potential in antiviral drug development. This research provides a foundation for utilizing HMOs as a natural source for designing new therapeutics, offering a novel approach in the fight against respiratory viral infections.</span></p>
Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn
<p>Breast cancer has become most prevalent disease and their incidence has doubled in Indian scenario. Targeted therapy with the novel compounds derived from plants could be the promising approach for the development of drugs. <em>Euphorbia thymifolia</em> L is a widely growing tropical herb which has been reported for its various ethnopharmacological properties, including anticancer properties. The aim of the present study was to identify the active phytocompounds present in the methanolic extract using an <em>I</em><em>n-silico</em> approach. The methanolic extract of <em>E. thymifolia</em> (ME.ET) was subjected to GC-MS analysis and the identified compounds were docked with potential protein targets implicated in breast cancer such as ERK1, AKT, EGFR/HER2, ER, MELK, PLK1, PTK6. Compounds with good docking score were further subjected to dynamics study to understand the protein ligand binding stability, ligand pathway calculation, molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculation using Schrodinger suite. Out of 219 unique phytocompounds subjected to docking, two compounds namely, 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino)ethyl 4-isopropylphenyl ester (SADPE) showed good docking score. Molecular dynamics study showed high affinity and low binding energy for TTDB with HER2, ERK1 and SADPE with ER. Hence this is the first study to identify and report active compounds from <em>E.thymifolia</em> linn. Further <em>invitro</em> and <em>invivo</em> anticancer studies can be performed to confirm these results and understand the molecular mechanism by which TTDB and SADPE exhibit anticancer activity against breast cancer.</p>
DATASET: Using a Bacterial Protein to Selectively Target Bacterial Biofilms: Treatment of S. epidermidis Biofilms with Targeted Photothermal Gold Nanoparticles
<p>Supporting data for the manuscript.</p>
Molecular docking analysis was performed to assess the affinity of onalespib for their targets LOX, elucidating binding poses, protein interactions, and associated binding energies.
<p>To analyze the binding affinities and interaction modes between the drug candidates and their targets, we employed the Autodock Vina software [21]. Molecular structures of the candidate drugs and targets of hub genes were retrieved from Pubchem (https://pubchem.ncbi.nlm.nih.gov/) and Protein Data Bank database (http://www.rcsb.org/), respectively. <span>In the analysis of docking, the files for all proteins and molecules were converted to PDBQT format. Water molecules were removed and polar hydrogen atoms were added. The grid box was positioned at the center to encompass the protein domain, allowing for unrestricted movement of molecules.</span></p>
Targeting protein-ligand neosurfaces using a generalizable deep learning approach [benchmark dataset]
<p>PDB files and processed surface meshes for the binder recovery benchmark. For the larger PDBbind decoy set only the PDB files are provided.</p>
Results for Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast
<p>This dataset contains the original results for the paper "Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast". To reproduce all figures in this paper, this dataset is required. The scripts can be found in Github (https://github.com/SysBioChalmers/pcSecYeast)</p>
Binding networks identify targetable protein pockets for mechanism-based drug design
<p>This repository contains supporting files for the manuscript entitled: Binding networks identify targetable protein pockets for mechanism-based drug design.</p>
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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.