Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
108
datasets available to search
ShareScore release 0.9.0
Dataset results
108 results for “ion channel”
Human Hyperpolarization Activated Cyclic Nucleotide Gated Ion Channel 4 (HCN4); A Target Enabling Package
<p>HCN4 is one of four hyperpolarisation activated cyclic nucleotide gated ion channels. It is responsible for the pacemaker or funny (If) current in the heart and is required for maintenance of a stable heartbeat. Mutations in HCN4 lead to a number of arrhythmias. HCN4 is the target for the angina drug ivabradine, which reduces HCN4 activity. However, ivabradine is non-selective, affecting all of the four HCN channels. HCN4 is a close homologue of HCN2, which is a target for neuropathic and inflammatory pain treatment. We have solved the structure of HCN4 both in complex with cyclic AMP and without nucleotide. Comparison of our HCN4 structure with that of the related HCN1 channel (86% identity) allows us to suggest ways to design selectivity for small molecule inhibitors between these closely related channels. </p>
Dataset of molecular docking data of neuropeptides to acid-sensing ion channels
<p>The *.dock4 files are result files of molecular docking with the software Autodock Vina to the human ASIC1a closed state model, of the peptides FRRFa and KNFLRFa (FRRF.dock4, KNFLRF.dock4) that can be visualized with structure viewing programs such as UCSF Chimera on the closed ASIC1a model file (closed_ASIC_pH7.4.pdb). The file “FRRF_KNFLRF_complexes.pdb” provides the structures of selected poses of FRRFa and KNFLRFa peptides docked to the closed conformation of the human ASIC1a model.</p>
Ion permeation through a narrow cavity constriction in KCNQ1 channels, scours files of MD simulations and analysis of electrophysiological experiments.
<p>Source files of Molecular Dynamic (MD) simulations and analysis files of electrophysiology data in Igor pro software format. KCNQ1 channel pore region (G245-K354) was embedded in a lipid bilayer consisting of phosphatidylcholine phospholipids (POPC) and ion permission mechanism was analized by MD simulations using the computational electrophysiology (compEL) method implemented in GROMACS v2022.4. Ion imbalance between compartments of double-membrane system created a membrane potential of abour 300 mV which drives ion movment.</p>
Probing Ion Channel Functional Architecture and Domain Recombination Compatibility by Massively Parallel Domain Insertion Profiling
<p>Supplementary Data for a large insertional profiling study described in Coyote-Maestas et al. (2021) Nature Communications.</p>
Molecular Dynamics Simulations of Hydrophilic (QTY) Potassium Ion Channels in Water
<p>You can find here the molecular dynamics (MD) trajectories of QTY proteins in water performed for the "Computational engineering of water-soluble potassium ion channels through QTY transformation" manuscript. Please cite our paper and the previous Zenodo dataset when referring to or using this data. If you have any questions, please contact me (Eva Smorodina) at ribes.ev@gmail.com. Thank you!<br><br>Smorodina, E. (2024). Molecular Dynamics Simulations of Hydrophobic (cryo-EM and Native) and Hydrophilic (QTY) Potassium Ion Channels [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10592842</p>
Piezo1 ion channels are capable of conformational signaling
<p>Piezo1 is a mechanically activated ion channel that senses forces with short latency and high sensitivity. Piezos undergo large conformational changes, induce far-reaching deformation onto the membrane, and modulate the function of two-pore potassium (K<sub>2P</sub>) channels. Taken together, this led us to hypothesize that Piezos may be able to signal their conformational state to other nearby proteins. Here, we use chemical control to acutely restrict Piezo1 conformational flexibility and show that Piezo1 conformational changes, but not ion permeation through it, are required for modulating the K<sub>2P</sub> channel TREK1. Super-resolution imaging and stochastic simulations further reveal that both channels do not co-localize, which implies that modulation is not mediated through direct binding interactions; however, at high Piezo1 densities, most TREK1 channels are within the predicted Piezo1 membrane footprint, suggesting the footprint may underlie conformational signaling. We speculate that physiological roles originally attributed to Piezo1 ionotropic function could, alternatively, involve conformational signaling.</p>
X-ray scattering datasets associated with the publication "Side chain length dependent dynamics and conductivity in self assembled ion channels"
<p>X-ray scattering datasets for samples described in the 2022 publication "Side chain length dependent dynamics and conductivity in self assembled ion channels". This dataset includes both raw and processed X-ray scattering data for samples ILC8, ILC10, ILC12, ILC14 and ILC16 alongside background measurement files (BKG).</p>
A large comprehensive curated dataset of small molecules and their activities covering three cardiac ion channels: hERG, Cav1.2, and Nav1.5
<p>The compressed data folder (dataset.rar) represents a data framework for researchers in the field of drug discovery to perform in depth analyses on a very large open-access unique and comprehensive hERG, Nav1.5, and Cav1.2 cardiotoxicity integrated database of small molecules and their activities. The database is organized as follows:</p> <ul> <li>Each sub-folder represents a cardiac ion channel target: hERG, Nav1.5, and Cav1.2</li> <li>Each target sub-folder consists of 3 files in CSV format: One file containing the development set (split into training and validation sets using an 80/20 ratio for hyperparameter tuning). The other 2 files contain external evaluation sets. The first test dataset consists of compounds with a structural similarity of no more than 60% (Tanimoto similarity ≤ 0.6) to the remaining development set, while the second test dataset comprises compounds with a structural similarity of no more than 70% (Tanimoto similarity ≤ 0.7) to the remaining development set.</li> <li>Each file contains data with 7 columns: "InChl Key" as a unique identifier of the chemical structure, "SMILES" as the string format of storage and exchange of the chemical structure, "Source" as the upstream data source from which the data was retrieved, "ChEMBL ID" as the ChEMBL identifier if the compound comes from ChEMBL database, "PubChem CID" as the PubChem compound identifier if the compound comes from PubChem database, "pIC50" as the negative logarithm of the half-maximal inhibitory concentration (IC50) to describe the potency of the compound, and "USED_AS" column specifying whether the compound was used for training or validation.</li> </ul> <p><strong>Upon usage, please cite this publication:</strong></p> <ul> <li>Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled Barakat, Wout Bittremieux, <strong>Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction</strong>, <em>Journal of Chemical Information and Modeling</em>, (2023). doi:<a href="https://doi.org/10.1021/acs.jcim.3c01301">10.1021/acs.jcim.3c01301</a></li> </ul> <p> </p>
Piezo1 ion channels are capable of conformational signaling
Open the record for dataset details and reuse information.
Data from: Blood pressure pulsations modulate central neuronal activity via mechanosensitive ion channels
<p><span>The transmission of heartbeat through the cerebral vascular system is known to cause intracranial pressure pulsations. Here we report that arterial pressure pulsations can directly modulate central neuronal activity. </span><span>In a semi-intact rat brain preparation, vascular pressure pulsations elicit correlated local field oscillations in the olfactory bulb (OB) mitral cell layer. These oscillations do not require synaptic transmission, but reflect baroreceptive transduction in mitral cells. This transduction is mediated by an excitatory mechanosensitive ion channel and modulates neuronal spiking activity. Indeed, in awake animals, the heartbeat entrains the activity of a subset of OB neurons within ~20 ms. Thus, we propose that this fast intrinsic interoceptive mechanism can modulate perception, e.g. during arousal, within the OB and also possibly across various brain areas.</span></p>
Touch sensation requires the mechanically-gated ion channel Elkin1
<p>The extraordinary speed of touch perception is enabled by mechanically-activated ion channels, the opening of which excites cutaneous sensory endings to initiate sensation. We identify Elkin1(1) as an ion channel likely gated by mechanical force necessary for normal behavioral touch sensitivity in mice. Touch insensitivity in Elkin1-/- mice was caused by a loss of mechanically-activated currents (MA-currents) in around half of all sensory neurons that are activated by light touch (low threshold mechanoreceptors, LTMRs). Reintroduction of Elkin1 into sensory neurons from Elkin1-/- mice acutely restored MA-currents. Additionally, siRNA mediated knockdown of Elkin1 from induced human sensory neurons substantially reduced indentation-induced MA-currents supporting a conserved role for Elkin1 in human touch. Our data identify Elkin1 as a novel core component of touch transduction in mammals.</p>
Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold
<p>Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (Na<sub>V</sub>) channel - Na<sub>V</sub>1.8, human voltage-gated calcium (Ca<sub>V</sub>) channel – Ca<sub>V</sub>1.1, and human voltage-gated potassium (K<sub>V</sub>) channel – K<sub>V</sub>1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of Na<sub>V</sub>1.8, Ca<sub>V</sub>1.1, and K<sub>V</sub>1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.</p>
Square Antiprismatic Ion Chelation Is a Key Determinant for Potassium Channel Selectivity
<p>Files presented here are archives K_DB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz.</p> <p>Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul>
Mechanism of Praziquantel action at a parasitic flatworm ion channel
<p>Data supporting Park <em>et al.</em> [Mechanism of praziquantel action at a parasitic flatworm ion channel]</p> <p> </p>
Tyrosine phosphorylation tunes chemical and thermal sensitivity of TRPV2 ion channel
<p><span>Transient receptor potential vanilloid 2 (TRPV2) is a multimodal ion channel implicated in diverse physiopathological processes.</span><span> Its important involvement in immune responses has been suggested such as in the macrophages' phagocytosis process. However, the endogenous signaling cascades controlling the gating of TRPV2 remain to be understood. Here, we report that enhancing tyrosine phosphorylation remarkably alters the chemical and thermal sensitivities of TRPV2 endogenously expressed in</span><span> rat bone marrow-derived macrophages. We identify that the </span><span>protein tyrosine kinase </span><span>JAK1 mediates TRPV2 phosphorylation at the molecular sites Tyr(335), Tyr(471), and Tyr(525). JAK1 phosphorylation is required for maintaining TRPV2 activity and the phagocytic ability of macrophages. We further show that TRPV2 phosphorylation is dynamically balanced by protein tyrosine phosphatase</span><span> non-receptor type 1 (</span><span>PTPN1). PTPN1 inhibition increases TRPV2 phosphorylation, further reducing the activation temperature threshold. Our data thus unveil an intrinsic mechanism where the phosphorylation/dephosphorylation dynamic balance sets the basal chemical and thermal sensitivity of TRPV2. Targeting this pathway will aid therapeutic interventions in physiopathological contexts.</span></p>
Data from: Towards high-resolution modeling of small molecule - ion channel interactions
<p>Ion channels are critical drug targets for a range of pathologies, such as epilepsy, pain, itch, autoimmunity, and cardiac arrhythmias. To develop effective and safe therapeutics, it is necessary to design small molecules with high potency and selectivity for specific ion channel subtypes. There has been increasing implementation of structure-guided drug design for the development of small molecules targeting ion channels. We evaluated the performance of two Rosetta ligand docking methods, RosettaLigand and GALigandDock, on structures of known ligand - cation channel complexes. Ligands were docked to voltage-gated sodium (Na<sub>V</sub>), voltage-gated calcium (Ca<sub>V</sub>), and transient receptor potential vanilloid (TRPV) channel families. For each test case, RosettaLigand and GALigandDock methods were able to frequently sample a ligand binding pose within 1-2 Å root mean square deviation (RMSD) relative to the experimental ligand coordinates. However, RosettaLigand and GALigandDock scoring functions cannot consistently identify experimental ligand coordinates as top-scoring models. Our study reveals that the proper scoring criteria for RosettaLigand and GALigandDock modeling of ligand - ion channel complexes should be assessed on a case-by-case basis using sufficient ligand and receptor interface sampling, knowledge about state specific interactions of the ion channel and inherent receptor site flexibility that could influence ligand binding.</p>
Raw numerical data and cleavage assay blot for Figures found in the article: "The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord"
<p><span>In relation to our publication: "The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord" we provide all the individual quantitative observations that underlie the data summarized in the figures and results of our paper. More specifically we provide the data for <span><span>Fig. 1G, H, I, P, Q; Fig. 2D-G, R-U; Fig. 3E-H; Fig. 4D-F, Q-S; Fig. 5D-G, K-N; R-U; Fig. 6D-F, S-U; Fig. 7G, H, J-T; Fig. 8G-I, M, N, S, X, Y; Fig. 9D-G, R, S; Fig. 10D-Q, K-R; Fig. 11F, G; Fig. S2T-X; Fig. S3G; Fig. S4K, O, P and Fig. S6E-J</span></span></span>.</p> <p>In addition we provide a non-annotated and an annotated version of the original, uncropped gel picture shown in Fig. S4A</p>
Data from: Remote neurostimulation through an endogenous ion channel using a near infrared light-activatable nanoagonist
<p>The development of noninvasive approaches to precisely control neural activity in mammals is highly desirable. Here we utilized the ion channel TRPA1 as a proof of principle, demonstrating remote near-infrared (NIR) activation of endogenous channels in the neural structures of living mice through an engineered nanoagonist. This achievement enables specific neurostimulation in wild-type, non-genetically modified mice. Initially, target-based screening identified flavins as photopharmacological agonists, allowing for the photoactivation of TRPA1 in sensory neurons upon UVA/blue light illumination. Subsequently, upconversion nanoparticles (UCNPs) were customized with an emission spectrum aligned to flavin absorption and conjugated with flavin adenine dinucleotide, creating a nanoagonist capable of NIR activation of TRPA1. Following the intrathecal injection of the nanoagonist, noninvasive NIR stimulation allows precise bidirectional control of nociception in mice through the remote activation of spinal TRPA1. This study demonstrates a noninvasive NIR neurostimulation method with the potential for adaptation to various endogenous ion channels and neural processes by combining photochemical toolboxes with customized UCNPs.</p>
Alignment used for voltage gated ion channels phylogenetic analysis
<p>Alignment (performed with MAFFT) of sequences of voltage gated ion channels used to performe the phylogenetic analysis (PhyML SMS option) present in the supplementary figures.</p>
Datasets that simulated ion channel currents
<p>This repository contains pseudo-ion-channel current datasets described in the 2023 publication “Model-Free Idealization: Adaptive Integrated Approach for Idealization of Ion Channel Currents (AI2)”. The datasets simulate ion channel currents based on the two-state model (Gating Kinetics.tif) and contain two kinds of noise (experimental or white Gaussian noise) at different signal-to-noise ratios (SNRs=10.2, 5.14, and 1.82). Four values (1, 10, 100, and 1000 s<sup>-1</sup> ) were examined for k<sub>1</sub> and k<sub>2</sub> of the gating kinetics, yielding 16 combinations of k<sub>1</sub> and k<sub>2</sub> . The repository contains five time-series data for each combination of k<sub>1</sub> , k<sub>2</sub> , and SNR. Each dataset contains 5×10<sup>5</sup> points which correspond to a 20 s recording with a sampling frequency of 25 kHz.</p> <p><br> Time-series 0-1 (closed-open) sequences were first simulated using the QuB software. White Gaussian noise was added to the 0-1 sequence by Python 3.7. Experimental noise was added to the 0-1 sequence through electrophysiological recordings using a patch-clamp amplifier and a model cell (Molecular Devices). Voltage sequences consisting of V<sub>0</sub> and V<sub>1</sub> , which corresponded to the closed and open states, respectively, were input to the model cell (10 MΩ resister), and the resulting currents were recorded with the amplifier. Each CSV file has time, ground truth (0 or 1), and current.</p>
ScienceDex guides
Understand access before you commit
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.