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823 results for “kRas”
Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.
<p>Datasets related to the publication [1].<br> Including:</p> <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164) </li> </ul> <p><br> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. <em>PLoS Comput Biol Submitted</em> (2018)</p>
Distinct association of HRAS and KRAS with Mn(II) ion illustrated by paramagnetic NMR
<p><a name="OLE_LINK4"></a><span>RAS proteins are among crucial oncogenic proteins and are involved in several essential intracellular processes. The RAS protein has an intrinsic metal binding site for Mg<sup>2+</sup>, which is important for the conformational stability of the active site. Recently, it was reported that a second metal ion binding site, located further from the active site in HRAS, binds Ca<sup>2+</sup> with millimolar affinity.</span><span> As one of the most abundant metal ions in cells, Mn<sup>2+</sup> is a potential candidate for the second metal ion binding site in RAS proteins. Here, we examined the interaction of Mn<sup>2+</sup> with HRAS and KRAS using high resolution NMR spectroscopy. The NMR data showed that both the second metal ion binding site and the switch I and II regions bind Mn<sup>2+</sup> in the RAS proteins. Furthermore, our paramagnetic NMR results disclosed the conformational differences in helix </span><span>a</span><span>3 and the following loop between HRAS and KRAS, accompanied by the association with metal ion binding. These results provide new insights into the interaction of RAS proteins and Mn<sup>2+</sup> in the respective biological processes in cells.</span></p>
Illuminating oncogenic KRAS signaling by multi-dimensional chemical proteomics
<p><span>Mutated KRAS is among the most frequent activating genetic alterations in cancer. Drug discovery efforts have led to inhibitors that block mutant KRAS activity. To better understand the molecular basis of their cytostatic rather than cytotoxic effects, w</span>e performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement, and protein expression characterization in response to KRAS, MEK, ERK, SHP2, and SOS1 inhibitors in pancreatic (KRAS G12C, G12D) and lung cancer (KRAS G12C) cell lines. Analysis of the dose-response curves available online revealed common and cell line-specific signaling networks dominated by KRAS activity. Time-dose experiments separated early ERK-driven effects from those that result from cell cycle arrest. The transition occurred without substantial proteome re-modelling but extensive changes in phosphorylation and ubiquitinylation. Our resource highlights the complexity of KRAS signaling in cancer and places a large number of new proteins and their modifications into this functional context for further exploration.</p> <p>We provide all dose-response curve data processed using internal pipelines or CurveCurator v0.5.0 (<a href="https://github.com/kusterlab/curve_curator" target="_blank" rel="noopener">https://github.com/kusterlab/curve_curator</a>). A README file is included with details about each file and a Meta table describing the experimental conditions. Each CurveCurator folder contains both the input data (including the TOML parameter file used for curve generation) and the output, which includes interactive dashboards (<strong>dashboard.html</strong>) and processed curve data (<strong>curves.txt</strong>).</p> <p>Phospho-proteome, whole proteome, ubiquitinome, Kinobead pulldown, and cysteine profiling data are provided in separate ZIP folders. Additionally, we include all aggregated supplementary tables and analysis output tables used for figure generation in the manuscript.</p>
Generation of KRAS knockout pancreatic cancer cell line PANC1
<p>We used CRISPR to inactivate mutant KRAS and STAT3 in PANC1 (KRASG12D) pancreatic cancer cell line. Gene expression analysis of KRAS intact vs. knockout cells identified sets of genes involved in protein synthesis, cell differentiation, and metabolic processes, while the expression of MAPK/ERK target genes remained unperturbed.</p>
Molcular Dynamics Data for Therapeutic High Affinity T Cell Receptor Targeting a KRAS G12D Cancer Neoantigen
<p>This folder contains the starting structures and input scripts required to simulate the wild-type and G12D KRAS peptide bound TCR-pHLA complexes, as performed in this study.</p> <p><br> Starting_Structures - This folder contains the amber parameter/topology files used to simulate each system (.prmtop) and the coordinates of the starting structure both as amber coordinate file (.rst) and PDB file (.pdb).<br> MD_Inputs - This folder contains the amber MD inputs used to run the md simulations. <br> MMPBSA_inputs - This folder contains the input files for running MMPBSA with the MMPBSA.py script in amber. The mmpbsa.in script was used for calculating overall binding energy whereas the mmpbsa_decomp.in script was used for calculating the per-residue contribution to binding energy. </p>
Dataset II related to the publication: In silico Evaluation of the Thr58-associated Conserved Water with KRAS Switch-II Pocket Binders
<p>Desmond trajectories of simulations conducted with TIP3P water model related to the publication:</p> <p>Leini R, Pantsar T: In Silico Evaluation of the Thr58-Associated Conserved Water with 2 KRAS Switch-II Pocket Binders. J. Chem. Inf. Model. [accepted] https://doi.org/10.1021/acs.jcim.2c01479</p> <ul> <li>Individual .zip files contain the Desmond trajectories and -out.cms -files.</li> </ul> <p>Related datasets: 10.5281/zenodo.7656467 and 10.5281/zenodo.7342311</p>
Dataset III related to the publication: In silico Evaluation of the Thr58-associated Conserved Water with KRAS Switch-II Pocket Binders
<p>Desmond trajectories of simulations conducted with TIP4P water model related to the publication:</p> <p>Leini R, Pantsar T: In Silico Evaluation of the Thr58-Associated Conserved Water with 2 KRAS Switch-II Pocket Binders. J. Chem. Inf. Model. [accepted] https://doi.org/10.1021/acs.jcim.2c01479</p> <ul> <li>Individual .zip files contain the Desmond trajectories and -out.cms -files.</li> </ul> <p>Related datasets: 10.5281/zenodo.7656467 and 10.5281/zenodo.7341954</p>
Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"
<p>Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available <a href="https://doi.org/10.1101/2022.08.15.503960">here</a>)</p> <p><strong>Analysis of AP-MS data</strong>: analysis.zip</p> <p>Contains the following scripts as well as their outputs:</p> <ul> <li>01_preparation.R R script for filtering and processing our mass spec data.</li> <li>02_diffbinding.R R script for differential analysis followed by gene set enrichment.</li> <li>03_funcstats.R R script for statistical analysis over different ontology terms.</li> <li>04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03.</li> <li>05_1_random_walks.py Python script for performing random walks for specific functional terms.</li> <li>05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1.</li> </ul> <p>The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD035399">entry</a>.</p> <p>Interactive visualization of the results of most of this analysis is available on <a href="https://github.com/PhilippJunk/kras_apms_vis">GitHub </a>as a Shiny app.</p> <p> </p> <p><strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip</p> <p>Contains the following script, as well as its output:</p> <ul> <li>01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances.</li> </ul> <p>The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD039404">entry</a>.</p>
Dataset I related to the publication: In silico Evaluation of the Thr58-associated Conserved Water with KRAS Switch-II Pocket Binders
<p>WaterMaps results related to the publication:</p> <p>Leini R, Pantsar T: In Silico Evaluation of the Thr58-Associated Conserved Water with 2 KRAS Switch-II Pocket Binders. J. Chem. Inf. Model. [accepted] https://doi.org/10.1021/acs.jcim.2c01479</p> <ul> <li>Individual .zip files contain the WaterMap results for each structure.</li> </ul> <p><em>Additional notes: there is a typo in the 5v90 file name (it is the 5v9o structure).</em></p> <p>Related datasets: 10.5281/zenodo.7341954 and 10.5281/zenodo.7342311</p>
Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
<p><span>Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the <a>interactions </a></span><span>between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged—the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context—and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.</span></p>
Binimetinib and Hydroxychloroquine in Patients With Advanced KRAS Mutant Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT04735068. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Trametinib and Docetaxel in Treating Patients With Recurrent or Stage IV KRAS Mutation Positive Non-small Cell Lung Cancer
ClinicalTrials.gov study NCT02642042. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Assess Efficacy & Safety of Selumetinib in Combination With Docetaxel in Patients Receiving 2nd Line Treatment for v-Ki-ras2 Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) Positive NSCLC
ClinicalTrials.gov study NCT01933932. IPD Sharing: YES. Countries: 26. Publications: 2.
Phase 3 Study of MRTX849 (Adagrasib) vs Docetaxel in Patients With Advanced Non-Small Cell Lung Cancer With KRAS G12C Mutation
ClinicalTrials.gov study NCT04685135. IPD Sharing: NO. Countries: 23. Publications: 1.
FOLFOXIRI Plus Panitumumab Patients With Metastatic KRAS Wild-Type Colorectal Cancer With Liver Metastases Only
ClinicalTrials.gov study NCT01226719. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Selumetinib in Patients Receiving Pemetrexed and Platinum-based Chemotherapy in Advanced or Metastatic KRAS Wildtype or Unknown Non-Squamous NSCLC
ClinicalTrials.gov study NCT02337530. IPD Sharing: NO. Countries: 1. Publications: 1.
CAPOX in KRAS Wild-Type Advanced Adenocarcinoma of the Small Bowel or Ampulla of Vater
ClinicalTrials.gov study NCT01202409. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study Evaluating Biomarkers in Patients With Colorectal Cancer and Native KRAS Treated With Chemotherapy + Cetuximab
ClinicalTrials.gov study NCT01276379. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Onvansertib in Combination With FOLFIRI and Bevacizumab for Second Line Treatment of Metastatic Colorectal Cancer Patients With a KRAS Mutation
ClinicalTrials.gov study NCT03829410. IPD Sharing: NO. Countries: 1. Publications: 3.
A Study of Abemaciclib (LY2835219) in Participants With Previously Treated KRAS Mutated Lung Cancer
ClinicalTrials.gov study NCT02152631. IPD Sharing: YES. Countries: 21. Publications: 2.
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.