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Dataset results
28 results for “drug binding”
Drug molecules binding to Covid-19 main protease
<p>A comparative look at where drug molecules bind to the main protease of Covid-19 depicted by interactive raytracing in the UnityMol software. The visualization is inspired by the animation of small molecules in 92 protein databank structures (<a href="https://www.rbvi.ucsf.edu/chimerax/data/sars-protease-may2020/">https://www.rbvi.ucsf.edu/chimerax/data/sars-protease-may2020/</a>) prepared by the ChimeraX team.</p>
Dataset for identification of peptidomimetics and FDA approved drugs binding to novel allosteric pocket of the IRE1 RNase domain.
<p>Input files, protein-peptide and ligand docking datasets, and simulation trajectories, compressed in "rar" format. All calculations performed using the Schrödinger 2020-2 / 2020-3 software (modules Glide, Phase, Desmond). </p> <p>SI includes folders:</p> <p>1- "Peptide" folder contains the best peptide "Docking" complexes and "Pharmacophore" models </p> <p>2-"Quercitrin" folder contains the molecular "Docking", "MMGBSA" calculations, and "MD" simulation</p> <p>3-"Pemetrexed" folder contains the molecular "Docking", "MMGBSA" calculations, and "MD" simulation</p> <p> </p>
Binding constants of clinical drugs and other organic ligands with human and mammalian serum albumins
<p>The dataset contains literature values of the experimental equilibrium binding constants of drugs and some other organic ligands with human and mammalian (predominantly bovine) serum albumins. There are 1755 records gathered from 346 original literature sources describing the albumin affinity of 324 different substances. The data were extracted from both articles and existing protein binding databases applying strict data selection rules in order to exclude the values influenced by the third-party compounds. For each experiment with a particular ligand–albumin system found in literature we provide (if possible) the following details: albumin source organism, ligand chemical name, canonical SMILES, InChIKey, the binding (either association <em>K<sub>a</sub></em> or dissociation <em>K<sub>d</sub></em>) constant value in molarity-based scale, temperature in K, albumin and ligand concentrations, buffer pH, composition, and concentration, experimental method, model used for the binding constant calculation, DOI or link to the source paper. For the results obtained using independent binding sites model, the average number of binding sites <em>n</em> is also provided. If two different types of binding sites were suggested, we put the second site-specific binding constant <em>K<sub>a2</sub></em> or <em>K<sub>d2</sub></em> and the number of the second-type sites<em> </em> <em>n</em><sub>2</sub> into separate columns. For some systems, the enthalpies of binding have also been determined either from the temperature dependence of the binding constant or using direct calorimetric measurements. Their values are also given in the respective column. The dataset can be used as the reference one, for the development of predictive models to calculate the binding constants, and for the choice of the experimental setup in the future albumin binding studies.</p>
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
<p>Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints".</p> <p>The directory is fully documented with README files.</p> <p>Differences of V2.0 with V1.0:</p> <ul> <li>Due to a software bug we had to re-parametrize the ligands whose torsions were parametized with ANI-2.X (ligand 6 and 7).</li> <li>During the peer reviewing process we also parametrized with ANI-2.X and docked ligand 8.</li> </ul>
A Comprehensive Dataset of protein-protein interactions and Ligand Binding Pockets for Advancing Drug Discovery
<p>This dataset presents a comprehensive collection of structural data related to protein-protein interactions (PPIs) and ligand binding pockets. The dataset includes high-quality structural information that can aid researchers in the fields of bioinformatics, structural biology, and drug discovery. It encompasses a diverse set of PPI complexes and associated ligands, enabling detailed investigations into molecular interactions at the atomic level. This article introduces an indispensable resource designed to unlock the full potential of PPIs while pioneering a novel metric for pocket similarity for repurposing protein partners.</p>
PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery
<p>Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.</p> <p>Codes for PPB-Affinity database preparation is disclosed at <a title="https://github.com/Huatsing-Lau/PPB-Affinity-DataPrepWorkflow" href="https://github.com/Huatsing-Lau/PPB-Affinity-DataPrepWorkflow">https://github.com/Huatsing-Lau/PPB-Affinity-DataPrepWorkflow</a>.<br>Codes for the benchmark algorithm is disclosed at <a href="https://github.com/ChenPy00/PPB-Affinity">https://github.com/ChenPy00/PPB-Affinity</a>.</p> <p>The article related to the PPB-Affinity dataset can be found at <a href="https://doi.org/10.1038/s41597-024-03997-4">https://doi.org/10.1038/s41597-024-03997-4</a>.</p> <p>Files are orginized as follows:</p> <p><a href="13054646" target="_blank" rel="noopener noreferrer">- PPB-Affinity.xlsx</a></p> <p><a href="13054646" target="_blank" rel="noopener noreferrer">- samples_deleted.zip</a></p> <p><a href="../api/records/13067409/draft/files/PPB-Affinity-AF.zip/content" target="_blank" rel="noopener noreferrer">- PPB-Affinity-AF.zip</a></p> <p>- PDB/</p> <p> - Affinity Benchmark v5.5/</p> <p> - file1.pdb</p> <p> - file2.pdb</p> <p> - ...</p> <p> - filek.pdb</p> <p> - ATLAS/</p> <p> - PDBbind v2020/</p> <p> - SAbDab/</p> <p> - SKEMPIv2.0/</p>
PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport
<p>These data were generated to investigate the effect of point mutations in PfCRT on the kinetics of chloroquine and piperaquine binding and transport. The protein confers resistance to a range of quinoline and quinoline-like antimalarials after the acquisition of certain amino acid substitutions, which occurs as a result of improper antimalarial use. The change in prescription from chloroquine (CQ) to piperaquine (PPQ) in Southeast Asian countries led to the emergence of a ninth mutation over the PfCRT Dd2 isoform, which renders the parasites resistant to piperaquine but re-sensitizes them to chloroquine. Despite structural information, how these individual mutations influence such opposing changes in the parasite's susceptibility to the aforementioned drugs remains unknown. Here, we show by biochemical studies that any of the piperaquine resistance-conferring mutations H97Y, F145I, M343L or G353V, either reduce the affinity of PfCRT Dd2 for CQ (Km) or reduce the efficiency of the transport cycle (Vmax). In parallel, they increase the Vmax, reduce the Km, or do both, in the case of PPQ transport. We also probed the binding cavity of PfCRT Dd2 and that of PfCRT Dd2_F145I, and found that it can readily bind both CQ and PPQ simultaneously, in a partial noncompetitive mechanism. We confirmed the latter finding through molecular docking and molecular dynamics simulations, describing for the first time the binding sites for both drugs in the cavity of PfCRT Dd2. With this, we found that the pocket where CQ binds seems to require an aromatic side chain, which is normally provided by F145, or by Y97 in the PPQ resistance-conferring H97Y mutant. Lastly, we generated an unnatural double mutant carrying both the H97Y and the F145I mutations. The engineered transporter displayed non-Michaelis-Menten kinetics both for CQ and PPQ transport and instead revealed sigmoidal kinetics, typical of proteins that bind substrate cooperatively. We thus provide new insights into the organization of the substrate-binding cavity of PfCRT and into the evolution of PfCRT.</p>
Data for: A cell surface-binding antibody atlas nominates a MUC18-directed antibody-drug conjugate for targeting melanoma
<p><span>Recent advances in targeted therapy and immunotherapy have substantially improved the treatment of melanoma. However, therapeutic strategies are still needed for unresponsive or treatment-relapsed melanoma patients. To discover antibody-drug conjugate (ADC)-tractable cell surface targets for melanoma, we developed an atlas of melanoma cell surface binding antibodies (pAbs) using a proteome-scale antibody array platform (PETAL). Target identification of pAbs led to development of melanoma cell killing ADCs against LGR6, TRPM1, ASAP1, and MUC18, among others. MUC18 was overexpressed in both tumor cells and tumor-infiltrating blood vessels across major melanoma subtypes, making it a potential dual-compartment and universal melanoma therapeutic target. AMT-253, an MUC18-directed ADC based on topoisomerase I inhibitor exatecan and a self-immolative T moiety, had a higher therapeutic index compared to its microtubule inhibitor-based counterpart and favorable pharmacokinetics and tolerability in monkeys. AMT-253 exhibited MUC18-specific cytotoxicity through DNA damage and apoptosis and a strong bystander killing effect, leading to potent antitumor activities against melanoma cell line and patient-derived xenograft models. Tumor vasculature-targeting by a mouse MUC18-specific antibody-T1000-exatecan conjugate inhibited tumor growth in human melanoma xenografts. Combination therapy of AMT-253 with an anti-angiogenic agent generated higher efficacy than single agent in a mucosal melanoma model. Beyond melanoma, AMT-253 was also efficacious in a wide range of MUC18-expressing solid tumors. Efficient target/antibody discovery in combination with the T moiety-exatecan linker-payload exemplified here may facilitate discovery of new ADC to improve cancer treatment</span><span>.</span></p>
Data for: A cell surface-binding antibody atlas nominates a MUC18-directed antibody-drug conjugate for targeting melanoma
Open the record for dataset details and reuse information.
PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport
Open the record for dataset details and reuse information.
Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development: Raw Diffraction Images (38 week soak). Zenodo
<p>The synchrotron raw diffraction images obtained at 38 weeks and wavelength 0.976 Å, illustrates the covalent coordination of the rhenium(I) tricarbonyl fragment to the His and Asp amino acid residues as well as movement along the solvent channels as described in the publication titled "Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development", written by Jacobs, Helliwell & Brink,<em> IUCrJ</em>, 2024, https://doi.org/10.1107/S2052252524002598.</p> <p>The raw diffraction images for the DLS data sets are made available at the Zenodo research data archive, as specified in the publication.</p>
Binding networks identify targetable protein pockets for mechanism-based drug design
<p>This repository contains supporting files for the manuscript entitled: Binding networks identify targetable protein pockets for mechanism-based drug design.</p>
This Study Will Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding In Brain Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT01258751. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of Increasing Doses of Cystine Binding Thiol Drugs on Cystine Capacity in Patients With Cystinuria
ClinicalTrials.gov study NCT02125721. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Pt-seq unveils the genomic binding pattern of platinum-based drugs [Pt-seq]
GEO Series GSE289501. Cricetulus griseus; Homo sapiens. 23 samples. Type: Other.
Interaction between cyclooxygenase-2 and caspase-3 abolishes the cleavage of RNA-binding protein HuR and promotes drug resistance in oral squamous cell carcinoma
GEO Series GSE79477. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Comparison between drugs- and unfolded proteins-induced responses reveals early induction of components of an ER-resident multimeric complex binding unfolded proteins
GEO Series GSE108346. Homo sapiens. 38 samples. Type: Expression profiling by array.
Global mapping of RNA-binding domains in multi-drug resistant Staphylococcus aureus
GEO Series GSE163719. Staphylococcus aureus subsp. aureus USA300. 12 samples. Type: Other.
Effects of the G-quadruplex-binding drugs Quarfloxin and CX-5461 on the malaria parasite Plasmodium falciparum
GEO Series GSE235142. Plasmodium falciparum. 9 samples. Type: Expression profiling by high throughput sequencing.
To Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding in Lung Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT02017730. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.