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40 results for “G protein-coupled receptor”
Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations
<p>Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity. </p> <p>You will find the following files:</p> <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>
Secretin-like class B G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 2463 quantitative mutation data points covering 13 secretin-like class B G protein-coupled receptors.</p> <p>Annotated according to GPCRdb standards (http://gpcrdb.org/), complemented by GPCRdb Ballesteros-Weinstein numbers assigned using GPCRdb KNIME nodes (https://github.com/3D-e-Chem/knime-gpcrdb).</p> <p>The data set is build from data sets published in:</p> <p>- Siu et al. Nature 2013, 499: 444-449. doi:10.1038/nature12393</p> <p>- Hollenstein, de Graaf et al. Tr Pharmacol Sci 2014, 35: 12-22. doi: 10.1016/j.tips.2013.11.001</p> <p>- Yang, de Graaf et al. J Biol Chem 2016, 291: 12991-3004. doi: 10.1074/jbc.M116.721977</p>
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1- MD simulations
<p>Topology, parameter and coordinates files of the Molecular dynamics (MD) simulations of OR5K1 3D models from AlphaFold 2 (AF2) and Homology Modeling (HM). We used ACEMD3 (v3.5.1) as a molecular engine, CHARMM36 as force field. Three replicas of 100 ns (dcd files) for both systems are reported. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) atoms were removed from the original trajectories before the upload.</p>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
Aminergic G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 6553 quantitative mutation data points covering 34 aminergic G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Kooistra et al. in BJP 2013, 170, 101.</p>
Chemokine G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 2004 quantitative mutation data points covering 10 chemokine G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Scholten et al. in BJP 2012, 165, 1617.</p>
Chemokine G protein-coupled receptor (GPCR) mutation data set - revision
<p>Curated set of 2004 quantitative mutation data points covering 10 chemokine G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Scholten et al. in BJP 2012, 165, 1617.</p> <p>Errors in the previous version were corrected and new data points for CCR2 and CCR9 were added.</p>
Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors - Scripts & Source data
<p>Source data and scripts to reproduce the figures that are part of the publication "Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors".</p> <p>Journal of Cell Science (2022) 135, jcs259685, DOI: 10.1242/jcs.259685</p> <p> </p> <p>An earlier version of this work is published as a preprint: "Heterogeneity and dynamics of ERK and Akt activation by G protein-coupled receptors depend on the activated heterotrimeric G proteins", DOI: <a href="https://doi.org/10.1101/2021.07.27.453948">10.1101/2021.07.27.453948</a></p>
Computational data for Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode
<p>MD simulation data for the research article titled "Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode".</p>
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
Open the record for dataset details and reuse information.
Asthma, Inflammation and G Protein-coupled Receptors (GPCR)
ClinicalTrials.gov study NCT00793676. IPD Sharing: Not stated. Countries: 1. Publications: 1.
G protein-coupled estrogen receptor stimulates human trophoblast cell invasion via YAP-mediated ANGPTL4 expression
GEO Series GSE183879. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning
GEO Series GSE144819. Homo sapiens; Escherichia coli. 27 samples. Type: Expression profiling by high throughput sequencing; Other.
Receptor quaternary organization explains G protein-coupled receptor family structure.
GEO Series GSE102461. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
The G Protein-Coupled Receptor ADGRG6 Maintains Mouse Growth Plate Homeostasis by Negatively Regulating IHH Signaling
GEO Series GSE275252. Mus musculus. 1 samples. Type: Other.
Transcriptome analysis of G protein-coupled receptors in distinct genetic subgroups of acute myeloid leukemia: identification of potential disease-specific targets
GEO Series GSE98310. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
Myocardial G protein-coupled receptor kinase 5 contributes to impaired cardiac function and immune cell recruitment in ischemic heart failure
GEO Series GSE132701. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
The G Protein-coupled Receptor P2Y14 Influences Insulin Release and Smooth Muscle Function in Mice
GEO Series GSE59285. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
beta-Arrestin Pathway-Selective G Protein-Coupled Receptor Agonists Engender Unique Biological Efficacy In Vivo
GEO Series GSE35181. Mus musculus. 18 samples. Type: Expression profiling by array.
Endometrial adhesion G protein-coupled receptors are dynamically expressed across the menstrual cycle and expression is altered by ovarian stimulation
GEO Series GSE220044. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
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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.