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Dataset results
873 results for “ligands”
Phase I/II Study of the Anti-Programmed Death Ligand-1 Durvalumab Antibody (MEDI4736) in Combination With Olaparib and/or Cediranib for Advanced Solid Tumors and Advanced or Recurrent Ovarian, Triple
ClinicalTrials.gov study NCT02484404. IPD Sharing: YES. Countries: 1. Publications: 3.
Evaluation of the Effect of Hypoglycemia With PET and a Norepinephrine Transporter Ligand
ClinicalTrials.gov study NCT02056249. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pilot Study Of Anti-Programmed Death Ligand-1 (Anti-PD-L1, Atezolizumab) In Asymptomatic Myeloma
ClinicalTrials.gov study NCT02784483. IPD Sharing: NO. Countries: 1. Publications: 1.
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: ‘Venus trapped, Mars transits’: Cu and Fe redox chemistry, cellular topography and in situ ligand binding in terrestrial isopod hepatopancreas
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Ligand-dependent effects of methionine-8 oxidation in parathyroid hormone peptide analogs
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Data from: A functionally conserved mechanism of modulation via a vestibule site in pentameric ligand-gated ion channels
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Gold Nanorods with PEG-Alkanethiol Ligands Etching in Graphene Liquid Cell Electron Microscopy-38 mM FeCl3
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Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (with unbound ligand)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer with unbound ligands. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Docking Adenosine Receptor Ligands to SARS-CoV2 mRNA Cap 2'-O-Methyltransferase: Energy Minimized Structures
<p>Energy minimized structures associated with a study docking adenosine receptor binders and related ligands to the adenosine binding site on SARS-CoV2 nsp16. The associated paper is under review, but we have a previous version of the paper available as a preprint at <a href="https://chemrxiv.org/articles/preprint/Docking_Adenosine_Receptor_Ligands_to_SARS-CoV2_mRNA_Cap_Guanine-N7_Methyltransferase/12462080/2">https://chemrxiv.org/articles/preprint/Docking_Adenosine_Receptor_Ligands_to_SARS-CoV2_mRNA_Cap_Guanine-N7_Methyltransferase/12462080/2</a>.</p>
Molecular dynamics simulation data of designed cyclic peptide (ligand-binding)
<p>Trajectories of ligand binding simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. <br> The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Data from: A large fraction of HLA class I ligands are proteasome-generated spliced peptides
The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced epitopes exist, but they have been regarded as rare events. Here, however, we show that the proteasome-generated spliced peptide pool accounts for one-third of the entire HLA class I immunopeptidome in terms of diversity and one-fourth in terms of abundance. This pool also represents a unique set of antigens, possessing particular and distinguishing features. We validated this observation using a range of complementary experimental and bioinformatics approaches, as well as multiple cell types. The widespread appearance and abundance of proteasome-catalyzed peptide splicing events has implications for immunobiology and autoimmunity theories and may provide a previously untapped source of epitopes for use in vaccines and cancer immunotherapy.
Supplemental material from: ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile
Estrogen insensitivity syndrome (EIS) arises from rare mutations in estrogen receptor α (ERα, encoded by ESR1 gene) resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. Here, we investigate known ESR1 mutants, Q375H and R394H, associated with EIS patients using in vitro and in vivo systems. Comparison of the transcriptome and DNA methylome from stable cell lines of both Q375H and R394H clinical mutants show a differential profile compared to WT ERα resulting in loss of estrogen-responsiveness. Molecular dynamic simulation shows that both ESR1 mutations change the ERα conformation of the ligand receptor complexes. Furthermore, we generated a mouse model Esr1-Q, harboring the human mutation using CRISPR/Cas9 genome editing. Female and male Esr1-Q mice are infertile and have similar phenotypes to αERKO mice. Overall phenotypes of the Esr1-Q mice correspond to those observed in the Q375H patient. Finally, we explore the effects of a synthetic progestogen and a GnRH inhibitor in the Esr1-Q mice for potentially reversing the impaired female reproductive tract function. These findings provide an important basis for understanding the molecular mechanistic consequences associated with EIS.
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.
Inferred stacking interactions for a dataset of proteins, nucleic acids and ligands
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Ligand-Free Pd-Catalyzed Direct C-H Arylation of Aryl Iodides under Ambient Air Conditions
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ApoDock: Ligand-Conditioned Sidechain Packing for Flexible Molecular Docking
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J-dimers of phthalocyanine analogues: structural characterization and their use for determination of association constants between ligands and central cation
<p>Dataset for manuscript: J-dimers of phthalocyanine analogues: structural characterization and their use for determination of association constants between ligands and central cation.</p>
A Folding–Docking–Affinity framework for protein–ligand binding affinity prediction
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NicheNet 2.0. Ligand-Target matrix and Networks
<p>NicheNet 2.0. ligand-target matrix and networks for both mouse and human</p>
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.