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2,012 results for “Kinase”
Data from: Protein kinase FaSnRK2.6 phosphorylates transcription factor FabHLH3 to regulate anthocyanin homeostasis during strawberry fruit ripening
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An unanticipated role for sphingosine kinase-2 in bone and in the anabolic effect of parathyroid hormone: Supplementary figures
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Restoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s linked-LRRK2 mutant mice
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Data from: A monomer-dimer switch modulates the activity of plant adenosine kinase
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Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters
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A lectin receptor-like kinase controls self-pollen recognition in Phlox
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Comment on "Ancient origins of allosteric activation in a Ser-Thr kinase"
<p>Hadzipasic <em>et al.</em> used ancestral sequence reconstruction to identify historical sequence substitutions that putatively caused Aurora kinases to evolve allosteric regulation. We show that their results arise from an implausible phylogeny and sparse sequence sampling. Addressing either problem reverses their inferences: allostery and the amino acids that confer it were not gained during the diversification of eukaryotes but were lost in a subgroup of Fungi.</p>
Classification of Binding Modes for Kinase-Inhibitor Complex Structures, 3D Activity Cliffs Formed by Kinase Inhibitors, and Structural Analogues of 3D-Cliff Compounds
<p>The classification of crystallographic binding modes is provided for 884 kinase-inhibitor complex structures that were assembled from PDB. In addition, a total of 105 three-dimensional activity cliffs formed by 3D kinase inhibitors are listed. Their corresponding potency information is also given. Furthermore, the 2D structural analogues of 3D cliff-forming inhibitors were identified from ChEMBL database, on the basis of matched molecular pairs. These analogs and their activity information are also provided.</p>
Kinase Inhibitors and Scaffolds
<p>On the basis of the assessment of compound and scaffold coverage of human kinome, sets of kinase inhibitors and scaffolds with high-confidence activity data assembled from ChEMBL release 18 are provided. In addition, sets of scaffolds involving in different types of structural relationships, having varying degrees of promiscuity and representing highly potent inhibitors are made available. A documentation file (i.e., README.txt) is given.</p> <p> </p>
The allosteric landscape of the Src kinase
<p>Fitness scores, MoCHI weights and miscellaneous files required to reproduce the analyses and figures in "The allosteric landscape of Src" (https://github.com/lehner-lab/src_allostery/blob/main/README.md) - Beltran A et al., 2025.</p>
Dataset of "Vertical pathway inhibition of receptor tyrosine kinases and BAD with synergistic efficacy in triple negative breast cancer"
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Kinex infers causal kinases from phosphoproteomics data
<p>Reference table of 82,755 pre-scored peptides containing serine and/or threonine phosphorylation sites for 303 kinases. This reference table is used as input for Kinex, a Python package, which infers causal serine/threonine kinases from phosphoproteomics data. <br><br>Kinex is released with the GNU General Public License, openly accessible to all users at https://github.com/bedapub/kinex.</p>
Supplementary Data: Uncovering DFG-out sequence propensity determinants of kinases with machine learning
<h2>General description</h2><p>This submission accompanies the paper "Uncovering DFG-out sequence propensity determinants of kinases with machine learning" and covers:</p><ul><li><strong>Trained models (train/models_latest)</strong>. A subset of these is also published as a part of the <a href="https://github.com/edikedik/kinactive">KinActive tool</a>; each model is of `KinactiveClassifier` type and can be loaded using this tool as well via `kinactive.io.load()` function).</li><li><strong>Patched sequences (patched_seqs)</strong>. PDB sequences, with missing regions patched by UniProt sequences. This is a collection of <a href="https://github.com/edikedik/lXtractor">lXtractor</a> ChainSequence objects.</li><li><strong>All labels, variables, and datasets</strong> (datasets and labels).</li><li><strong>Initial chains and predictions for SwissProt proteins</strong> (SP_predictions).</li></ul><h2>Note on model abbreviations</h2><p>The main text emphasized datasets that yielded more interpretable results. These were constructed from domain sequences, labeled as apo, inactive, DFG-in, or DFG-out, and further divided into TK and STK subsets. We refer to these datasets with the abbreviation <strong>AAIO</strong> (Apo All In or Out) to distinguish them from additional datasets.</p><p>In addition to <strong>AAIO</strong>, we explored two alternative labeling strategies:</p><ul><li><strong>AHAO</strong> (Apo/Holo Any Out): This dataset includes sequences from ligand-bound entries. All sequences within 95\% identity clusters are labeled as DFG-out if the cluster contains at least one sequence in this state. All others are labeled as DFG-in.</li><li><strong>AAO</strong> (Apo Any Out): This dataset excludes sequences corresponding to ligand-bound entries but includes those with conflicting conformational tendencies within 95\% identity clusters.</li></ul><p>Each of these datasets had two versions:</p><ol><li>A seed version, denoted by a "*" symbol.</li><li>A version enriched with orthologous sequences (no special designation).</li></ol><p>Together with the <strong>TkST</strong> datasets (encompassing TK and STK labels) used for testing the methodology, a total of 14 datasets were used, and both <i>RF</i> and <i>XGB</i> models were applied to each, using the same initial settings, resulting in 28 different models. This additional information is provided for completeness.</p>
Fig. 4 in Characterization of undescribed melanoma inhibitors from Euphorbia mauritanica L. cultivated in Egypt targeting BRAF and MEK 1 kinases via in-silico study and ADME prediction
Fig. 4. Experimental and TDDFT-simulated electronic circular dichroism spctra of (A) euphomauritanol A (1), (B) euphomauritanol B (2), and euphomauritanophane A (3).
Fig. 6 in Characterization of undescribed melanoma inhibitors from Euphorbia mauritanica L. cultivated in Egypt targeting BRAF and MEK 1 kinases via in-silico study and ADME prediction
Fig. 6. Bioavailability radar chart from Swiss ADME online web tool for compounds (A) 1, (B) 2 and (C) 3. The pink area represents the range of the optimal property values for oral bioavailability and the red line is compounds (A) 1, (B) 2 and (C) 3 predicted properties. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Characterization of undescribed melanoma inhibitors from Euphorbia mauritanica L. cultivated in Egypt targeting BRAF and MEK 1 kinases via in-silico study and ADME prediction
Fig. 5. (A) 2D binding mode, (B) 3D binding mode of Euphomauritanol A (1) in the active site of BRaf Kinase V600E (PDB ID: 4XV2) (C) 2D binding mode, and (D) 3D binding mode of euphomauritanophane A (3) in the active site of MEK 1 kinase (PDB ID: 4LMN).
Dataset related to publication: "Bromo-substituted indirubins for inhibition of protein kinase-mediated signalling involved in inflammatory mediator release in human monocytes"
<p>Dataset related to publication: Bachmann et al. "Bromo-substituted indirubins for inhibition of protein kinase-mediated signalling involved in inflammatory mediator release in human monocytes". Bioorganic Chemistry (2024) https://doi.org/10.1016/j.bioorg.2024.107470 </p> <ul> <li>Full Desmond MD simulation trajectories of the 10 replica simulations of compounds <strong>1</strong> and <strong>2</strong> bound to GSK-3beta (.zip files contain the -out.cms file and the trajectory)</li> <li>Maestro Glide XP docking output pose viewer files of compounds <strong>1 </strong>and <strong>2</strong> for CDKs (PDB IDs in the filenames)(.maegz -files)</li> </ul>
Dataset for manuscript Meier et al. 2024 -- Leveraging the Histidine Kinase-Phosphatase Duality to Sculpt Two-Component Signaling
<p>Dataset for manuscript Meier et al. 2024 -- Leveraging the Histidine Kinase-Phosphatase Duality to Sculpt Two-Component Signaling</p>
Simulation Data for Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination
<p>This is supporting information for an upcoming research manuscript. The uploaded tarball contains the directory structure needed to reproduce the simulations conducted to support the forthcoming article. The directory structure has three primary subdirectories, Alphafold which contains the initial structure predictions, Build, which has the Tcl scripts in VMD to assemble the system, and Simulation, which has the simulations themselves and the analysis. Since there is a limit to the file sizes that can be stored on Zenodo, we exclude many files to fit under the limit. The command to create the tarball was: <code>tar --exclude=LukeSim --exclude="*trr" --exclude="*dcd" --exclude="*GO*" --exclude="*HPR*" --exclude="*PGP*" --exclude="*GAT*" --exclude="*#" --exclude="*ppm" --exclude="*BAK" --exclude="*oldpgp*" -zcvf glykthermostable.tar.gz Thermostability/</code></p> <p>While the full trajectories are too large to be provided, reduced trajectories of only the protein component can be found in the <code>Thermostability/Simulation/Analysis/prottrajs</code> path. Files with the <code>.js</code> extension can be read via VMD.</p>
Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity
<p>Supplementary Figure S1. for IJMS</p>
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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)
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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.