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2,012 results for “Kinase”
Visualization results of Kinase-Ligand complex based on deep learning prediction score
<p>It contains all the validation results used in the manuscript "Global analysis of deep learning prediction using large-scale in-house kinome-wide profiling data". "ligand_list.smi" shows the compound structure information for each ligand, and the ligand atom weighting results for each target are stored in the "Targets" folder. PyMol can be used to visualize the results by using "load.py" (see readme for how to run it).</p>
Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket
<p>NMR raw <sup>1</sup>H-<sup>15</sup>N TROSY data and processed spectra of a titration of U-<sup>15</sup>N-labeled Abl<sup>83-534</sup> with imatinib presented in the manuscript "Imatinib disassembles the regulatory core of Abelson kinase by binding to its ATP site and not by binding to its myristoyl pocket".</p> <p><sup>1</sup>H-<sup>15</sup>N TROSY spectra were recorded at molar ratios of 0, 1:10, 3:10, 5:10, 7:10, 1:1, and 3:1 imatinib:Abl<sup>83-534</sup> at 303 K on a Bruker Ascend 600-MHz spectrometer equipped with a TCI triple resonance cryoprobe with 140 (<sup>15</sup>N) × 1024 (<sup>1</sup>H) complex points and acquisition times of 42 ms (<sup>15</sup>N) and 48 ms (<sup>1</sup>H).</p> <p><strong>Description of files contained in DATA.zip:</strong></p> <ol> <li>A3D.DAT: raw data in NMRPipe format with the 7 titration points stored a subsequent 2D planes</li> <li>B3D.DAT: processed data in NMRPipe format with the 7 titration points stored a subsequent 2D planes</li> <li>xy_3D.com: NMRPipe processing script to convert A3D.DAT to B3D.DAT</li> </ol>
Data from: Cyclin dependent kinase 5 (CDK5) regulates the circadian clock
<p>Circadian oscillations emerge from transcriptional and post-translational feedback loops. An important step in generating rhythmicity is the translocation of clock components into the nucleus, which is regulated in many cases by kinases. In mammals, the kinase promoting the nuclear import of the key clock component Period 2 (PER2) is unknown. We observed that the cyclin-dependent kinase 5 (CDK5) regulates the mammalian clock involving phosphorylation of PER2. Knock-down of Cdk5 in the suprachiasmatic nuclei (SCN), the main coordinator site of the mammalian circadian system, shortened the free-running period in mice. CDK5 phosphorylated PER2 at serine 394 (S394) in a diurnal fashion. This facilitated interaction with Cryptochrome 1 (CRY1) and nuclear entry of the PER2-CRY1 complex. Taken together, we found that CDK5 drives nuclear entry of PER2, which is critical for establishing an adequate circadian period of the circadian cycle. Therefore, CDK5 is critically involved in the regulation of the circadian clock.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - V142G mutant
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - A55G and V135G mutants
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
DUX4 expression activates JNK and p38 MAP kinases in myoblasts: MAJIQ splicing results
<p>Facioscapulohumoral muscular dystrophy (FSHD) is caused by misexpression of the DUX4 transcription factor in skeletal muscle that results in transcriptional alterations, abnormal phenotypes, and cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing (GEO GSE205421) paired with proteomics and phosphoproteomics (MassIVE MSV000089812). This analysis revealed changes in cellular physiology including DNA damage and altered mRNA splicing. Phosphoproteomic analysis uncovered widespread changes in protein phosphorylation rapidly following DUX4 induction indicating that alterations in kinase signaling may play a role in DUX4-mediated stress and cell death. Indeed, we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Inhibition of each of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover JNK as a novel pathway involved in DUX4-mediated cell death as well as provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.</p>
Data and Code for "Genomic mechanisms of resistance to tyrosine kinase inhibitors in HER2 amplified breast cancer"; Parsons et al. 2024
<p>Data and code for the manuscript <em>Genomic mechanisms of resistance to tyrosine kinase inhibitors in HER2 amplified breast cancer</em> (Parsons et al. 2024).</p> <p>Data: `parsons_her2_tki_data.tar.gz`</p> <p>Code: `parsons_her2_tki_code.tar.gz`</p> <p>The code may also be obtained from our GitHub repository:<br>https://github.com/getzlab/parsons_her2_tki_manuscript<br><br><br></p>
Potential Interactions of the 20 Arabidopsis thaliana Mitogen-Activated Protein Kinases (MPKs)
<p>A comprehensive dataset detailing potential interactions of the 20 <em>Arabidopsis thaliana</em> MPKs.</p>
Dynamics Playing a Key Role in the Covalent Binding of Kinase Inhibitors to the Focal Adhesion Kinase
Open the record for dataset details and reuse information.
A kinase fusion protein from Aegilops longissima confers resistance to wheat powdery mildew
<p>Many disease resistance genes have been introgressed into wheat from its wild relatives. However, reduced recombination within the introgressed segments hinders cloning of the introgressed genes. Here, we report the identification of wheat powdery mildew resistance gene <em>Pm13</em> originated from from <em>Aegilops longissima</em> using a method combining physical mapping with radiation-induced chromosomal aberrations and transcriptome sequencing analysis of ethyl methanesulfonate (EMS)-induced loss-of-function mutants. <em>Pm13</em> encodes a kinase fusion protein, designated MLKL-K, with an N-terminal domain of mixed lineage kinase domain-like protein (MLKL_NTD domain) and a C-terminal serine/threonine kinase domain bridged by a brace. The resistance function of <em>Pm13</em> is validated by transient and stable transgenic complementation assays. Transient over-expression analyses in <em>Nicotiana benthamiana</em> leaves and wheat protoplasts reveal that the fragment Brace-Kinase<sub>122-476</sub> of MLKL-K is capable of inducing cell death, which is dependent on a functional kinase domain and the three α-helices in the brace region close to the N-terminus of the kinase domain.</p>
Deformed Wing Virus interacts with host's arginine kinase to enhance viral replication in honey bees
<p><strong>Dataset used to plot the figures presented in the manuscript "Deformed Wing Virus interacts with host’s arginine kinase to enhance viral replication in honey bees".</strong></p> <p> </p> <p><strong>Abstract</strong></p> <p>Deformed wing virus (DWV) is a major bee pathogen that is actively transmitted by the parasitic mite <em>Varroa</em> <em>destructor</em> and plays a primary role in winter <em>Apis mellifera </em>colony losses. Despite intense investigation of this essential pollinator species, driven by its unique environmental and economic importance, the mechanisms underlying the molecular interactions between DWV and honey bees are still poorly understood. Here we report on a group of honey bee proteins, identified by mass spectrometry, that specifically co-immunoprecipitate with DWV virus particles. Most of the proteins identified are involved in fundamental metabolic pathways. Here we focused on Arginine kinase (ArgK), a conserved protein playing multiple roles both in physiological and pathological processes. We found that <em>ArgK</em> RNA levels positively correlate with DWV load in field-collected honey-bee larvae and adults and significantly increase in larvae and adults upon DWV injection in controlled laboratory conditions, indicating that the <em>ArgK</em> gene was upregulated by DWV infection. Silencing <em>ArgK </em>gene expression <em>in vitro</em>, using RNAi, resulted in reduced DWV viral load, thus demonstrating that ArgK function promotes the progression of DWV infection, likely altering the delicate balance between metabolism and immunity. In summary, these data indicate that successful DWV infection relies on transcriptional regulation and active recruitment of host ArgK by this viral pathogen. Therefore, our findings open novel perspectives on the potential control of DWV pathogenicity by targeting its interaction with specific host proteins.</p>
Structural insights into trypanosomatid Mnk kinase orthologues (kMnks) suggest altered mechanism in the kinase domain
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Set of selected compounds against DRAK2 kinase
<p>https://opennotebook.thesgc.org/first-set-of-selected-compounds-against-drak2-kinase/</p>
MOVIE#1 -Conduction in the Right and Left Ventricle is Differentially Regulated by Protein Kinases and Phosphatases: Implications for Arrhythmogenesis.
<p>Movie of paced activation acquired during perfusion of an isolated rabbit heart with CaMKII inhibitor KN93</p>
MOVIE#4 -Conduction in the Right and Left Ventricle is Differentially Regulated by Protein Kinases and Phosphatases: Implications for Arrhythmogenesis.
<p>Movie of arrhythmia acquired during perfusion of an isolated rabbit heart with PKA inhibitor H89.</p>
MOVIES#1-4 -Conduction in the Right and Left Ventricle is Differentially Regulated by Protein Kinases and Phosphatases: Implications for Arrhythmogenesis.
<p>Movies of paced activation and of arrhythmia acquired during perfusion of isolated rabbit hearts with CaMKII inhibitor KN93 or PKA inhibitor H89.</p>
MOVIE#3 -Conduction in the Right and Left Ventricle is Differentially Regulated by Protein Kinases and Phosphatases: Implications for Arrhythmogenesis.
<p>Movie of paced activation acquired during perfusion of an isolated rabbit heart with PKA inhibitor H89</p>
MOVIE#2 -Conduction in the Right and Left Ventricle is Differentially Regulated by Protein Kinases and Phosphatases: Implications for Arrhythmogenesis.
<p>Movie of arrhythmia acquired during perfusion of an isolated rabbit heart with CaMKII inhibitor KN93.</p>
Crystal structure of the LRR ectodomain from the plant immune receptor kinase SOBIR1 from Arabidopsis thaliana - native dataset
<p>This dataset includes the raw X-ray diffraction images collected on 02.02.2018 at beam line PXIII of the Swiss Light Source (SLS) Villigen, Switzerland. The dataset includes a .bz2 archive of the XDS processing, the resulting XDS_ASCII.HKL contains the integrated intensities. The corresponding coordinates and crystallographic structure factors have been deposited with the Protein Data Bank (http://rcsb.org) with ID 6R1H.</p>
Crystal structure of the LRR ectodomain from the plant immune receptor kinase SOBIR1 from Arabidopsis thaliana - sulphur SAD datasets
<p>This dataset includes the raw X-ray diffraction images collected on 06.11.2017 at beam line PXIII of the Swiss Light Source (SLS) Villigen, Switzerland. The archive native_images.tar contains a native dataset to 1.75 Å resolution (λ=1.033201 Å, 1 360° wedge at 0.1° oscillation). The archive ssad_images.tar contains redundant sulphur single-wavelength anomalous dispersion (SAD) data (λ= 2.078524 Å, 3 360° wedges at 0.1° oscillation) to 3.12 Å resolution. The xds_nat_ssad.tar.bz2 includes a .bz2 archive of the XDS processing for native and sulphur SAD data. Data were scaled together in xscale, the resulting xscale.hkl and nat1.hkl contain the integrated intensities and crystallographic structure factors. The corresponding coordinates have been deposited with the Protein Data Bank (http://rcsb.org) with ID 6R1H.</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)
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.