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ShareScore release 0.9.0
Dataset results
20 results for “ligand specificity”
Raw MS data for "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor"
<p>These are the raw HDX/MS data for our paper: "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor."</p>
Structural basis of ligand specificity and channel activation in an insect gustatory receptor
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Supplementary data for: Ligand-specific tuning of CLEC10A signalling strength and dendritic cell responses through engagement of different GalNAc-containing glycan structures
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DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model.
<p>test and training data.</p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
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Data from: High specificity in circulating tumor cell identification is required for accurate evaluation of programmed death-ligand 1
Background: Expression of programmed-death ligand 1 (PD-L1) in non-small cell lung cancer (NSCLC) is typically evaluated through invasive biopsies; however, recent advances in the identification of circulating tumor cells (CTCs) may be a less invasive method to assay tumor cells for these purposes. These liquid biopsies rely on accurate identification of CTCs from the diverse populations in the blood, where some tumor cells share characteristics with normal blood cells. While many blood cells can be excluded by their high expression of CD45, neutrophils and other immature myeloid subsets have low to absent expression of CD45 and also express PD-L1. Furthermore, cytokeratin is typically used to identify CTCs, but neutrophils may stain non-specifically for intracellular antibodies, including cytokeratin, thus preventing accurate evaluation of PD-L1 expression on tumor cells. This holds even greater significance when evaluating PD-L1 in epithelial cell adhesion molecule (EpCAM) positive and EpCAM negative CTCs (as in epithelial-mesenchymal transition (EMT)). Methods: To evaluate the impact of CTC misidentification on PD-L1 evaluation, we utilized CD11b to identify myeloid cells. CTCs were isolated from patients with metastatic NSCLC using EpCAM, MUC1 or Vimentin capture antibodies and exclusion-based sample preparation (ESP) technology. Results: Large populations of CD11b+CD45lo cells were identified in buffy coats and stained non-specifically for intracellular antibodies including cytokeratin. The amount of CD11b+ cells misidentified as CTCs varied among patients; accounting for 33–100% of traditionally identified CTCs. Cells captured with vimentin had a higher frequency of CD11b+ cells at 41%, compared to 20% and 18% with MUC1 or EpCAM, respectively. Cells misidentified as CTCs ultimately skewed PD-L1 expression to varying degrees across patient samples. Conclusions: Interfering myeloid populations can be differentiated from true CTCs with additional staining criteria, thus improving the specificity of CTC identification and the accuracy of biomarker evaluation.
Intra-op Detection of Occult Ovarian Carcinoma Using a Folate-Alpha Receptor Specific Fluorescent Ligand
ClinicalTrials.gov study NCT01511055. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR
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Data from: High specificity in circulating tumor cell identification is required for accurate evaluation of programmed death-ligand 1
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Age and ligand specificity influence the outcome of pathogen engagement on preleukemic and leukemic B cell precursor populations.
GEO Series GSE244018. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Effects of TLR4 ligands on inflammatory and lymphatic endothelial specific-cell gene expression in CD14+ PBMC
GEO Series GSE78162. Homo sapiens. 12 samples. Type: Expression profiling by RT-PCR.
Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs
GEO Series GSE94363. Homo sapiens. 84 samples. Type: Expression profiling by array.
Foam cell specific LXRα ligand
GEO Series GSE39079. Homo sapiens. 29 samples. Type: Expression profiling by array.
Dual role of signaling pathways in myeloma requires cell-type specific targeting of ligand-receptor interactions.
GEO Series GSE263702. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Gene expression of wild-type and Ppar-beta null primary keratinocytes, with and without infection with an activated Hras retrovirus, with and without the Ppar-beta specific ligand GW0742
GEO Series GSE32498. Mus musculus. 24 samples. Type: Expression profiling by array.
Regulation of nuclear gene expression by PK 11195, a ligand specific for the mitochondrial 18 kDa translocator protein (TSPO) (15, 30, and 45 minutes of exposure)
GEO Series GSE85697. Homo sapiens. 12 samples. Type: Expression profiling by array.
Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity [mouse]
GEO Series GSE98825. Mus musculus. 2 samples. Type: Expression profiling by array.
Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity
GEO Series GSE98826. Mus musculus; Homo sapiens. 4 samples. Type: Expression profiling by array.
Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity [human]
GEO Series GSE98814. Homo sapiens. 2 samples. Type: Expression profiling by array.
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.