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1,923 results for “compounds”
Supplementary material 1 from: Kola-Mustapha AT (2023) De novo design of pimarane diterpenoid compounds as potential alternatives to sarecycline for acne vulgaris treatment. Pharmacia 70(4): 1167-1176. https://doi.org/10.3897/pharmacia.70.e113065
Grid box within which Sandaracopimar-15-ene-6.beta., 8.beta.-diol binds is 192.5686 × 260.3472 × 119.6532 along the X, Y, Z-axis
Demo datasets for the protocol to identify shared transcriptional risks between diseases and compounds predicted to result in mutual benefit
<p>We present a computational protocol (https://github.com/ghbore/protocol-cancer-cvd-similarity), implemented as a Snakemake workflow, that was used in previous works (Gao et al., 2022; Baylis et al., 2023). This protocol allows researchers to identify shared transcriptional processes that drive disease and to screen existing compounds for mutual benefit. The protocol also includes a description of the pharmacovigilance study design used to validate the effect of novel compounds using electronic health records, where applicable. This repository bundles the datasets used in previous works as an example to run through the Snakemake workflow. These datasets include the TCGA cancer dataset, the STARNET and BiKE CVD datasets, and other dependent resources.</p>
Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn
<p>Breast cancer has become most prevalent disease and their incidence has doubled in Indian scenario. Targeted therapy with the novel compounds derived from plants could be the promising approach for the development of drugs. <em>Euphorbia thymifolia</em> L is a widely growing tropical herb which has been reported for its various ethnopharmacological properties, including anticancer properties. The aim of the present study was to identify the active phytocompounds present in the methanolic extract using an <em>I</em><em>n-silico</em> approach. The methanolic extract of <em>E. thymifolia</em> (ME.ET) was subjected to GC-MS analysis and the identified compounds were docked with potential protein targets implicated in breast cancer such as ERK1, AKT, EGFR/HER2, ER, MELK, PLK1, PTK6. Compounds with good docking score were further subjected to dynamics study to understand the protein ligand binding stability, ligand pathway calculation, molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculation using Schrodinger suite. Out of 219 unique phytocompounds subjected to docking, two compounds namely, 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino)ethyl 4-isopropylphenyl ester (SADPE) showed good docking score. Molecular dynamics study showed high affinity and low binding energy for TTDB with HER2, ERK1 and SADPE with ER. Hence this is the first study to identify and report active compounds from <em>E.thymifolia</em> linn. Further <em>invitro</em> and <em>invivo</em> anticancer studies can be performed to confirm these results and understand the molecular mechanism by which TTDB and SADPE exhibit anticancer activity against breast cancer.</p>
Optical constants, cross-sections, and supporting Python scripts for Fe L shell XAFS compounds in Corrales et al (2024), accepted to AAS Journals
<p>This Zenodo repository contains the data products and calculations of Corrales et al. (2024), https://arxiv.org/abs/2402.06726 (accepted to AAS Journals)</p> <p> </p> <p><strong>A WORD OF CAUTION</strong></p> <p>The cross-sections presented here have not been shifted in absolute energy scale. One of the key results from Corrales et al. (2024) is that the energy scale calibration for these compounds needs to be revisited. Please proceed with caution when using this information.</p> <p> </p> <h2>Optical Constants</h2> <p>kkcalc_products/ - This folder contains optical constants for the various compounds</p> <p>kkcalc_products/*_input.dat files contain the absorption as measured in Lee et al. (2009) https://ui.adsabs.harvard.edu/abs/2009ApJ...702..970L/abstract). These values are supplied as input to kkcalc (https://ui.adsabs.harvard.edu/abs/2014OExpr..2223628W/abstract, available at https://github.com/benajamin/kkcalc), along with the stoichiometric formula and material density for the compound of interest.</p> <p>kkcalc_products/*_refrac.dat files contain the kkcalc output, i.e., the real and imaginary parts of the complex index of refraction (m). The "Delta" column equals Re(1-m) and the "Beta" column equals Im(m).</p> <p> </p> <h2>Python Scripts</h2> <p>extinction_xsects.py - Calculates the extinction cross-section for an MRN distribution of dust</p> <p>These Python files from github.com/eblur/gastronomy are used by extinction_xsects.py in order to properly scale the mass column density to Fe abundance:</p> <ul> <li>abundances.py</li> <li>molecules.py</li> <li>minerals.py</li> </ul> <p> </p> <h2>Extinction Cross-sections</h2> <p>extinction_xsects/ - This folder contains the results of extinction_xsects.py</p> <p>extinction_xsects/*_FeL.pdf - A plot of the high resolution Fe L shell features</p> <p>extinction_xsects/*_broad.pdf - A plot of the broad band (0.3 - 10 keV), lower resolution cross-sections with 50 eV spacing. These cross-sections include extrapolations for the K and L shell features for other elements in the compounds based on Henke tables (see Watts et al. 2014)</p> <p>extinction_xsects/*_final.pdf - A plot of the consolidated (low resolution broad band and high resolution Fe L shell) extinction cross-sections</p> <p>extinction_xsects/*_xsect.fits - The final cross-section information for each compound, stored as fits file table. The table columns are energy, absorption optical depth, scattering optical depth, and extinction optical depth. All optical depths are scaled to have a total dust mass column of 1e-4 g cm^-2.</p>
Alkyl lipid distribution, elemental composition and compound-specific 14C isotope composition in marine and terrestrial sedimentary archives from sub-Antarctic South Georgia
<p>The dataset comprises elemental data, alkyl lipid data and radiocarbon (14C) data that was obtained on sediment samples from sub-Antarctic South Georgia. The sediments were collected from a range of different sites, including lakes, peat deposits, a marine inlet and a fjord during RV Polarstern expedition PS81 in 2013. More details on the study sites, sampling and data evaluation can be found in Berg et al. (submitted manuscript to JGR Biogeochemistry).</p>
Supporting Information for Cholinergic Selectivity of FDA-approved and Metabolite Compounds Examined with Molecular Docking-based Virtual Screening
<p><span>Typical docking configurations, detailed docking and visualization results for representative ligands and proteins. </span></p>
Compound coastal flooding in San Francisco Bay under climate change
<p>These files provide the data that are used for the compound coastal flooding analysis in San Francisco Bay under climate change.</p> <p>If you have used this dataset, please cite our papers:<br>"Wang, Z., Leung, M., Mukhopadhyay, S. <em>et al.</em> Compound coastal flooding in San Francisco Bay under climate change. <em>npj Nat. Hazards</em> <strong>2</strong>, 3 (2025). https://doi.org/10.1038/s44304-024-00057-0<em>"</em> . </p> <p>"Wang, Zhenqiang, et al. "A hybrid statistical–dynamical framework for compound coastal flooding analysis." <em>Environmental Research Letters</em> 20.1 (2024): 014005."</p>
Morphological profiling data resource enables prediction of chemical compound properties
<p><span><span>Morphological profiling with the Cell Painting assay has </span><span>emerged</span><span> as a promising method in drug discovery research. The assay captures morphological changes across various cellular compartments enabling the rapid prediction of compound </span></span><span><span><span>bioactivity</span></span></span><span><span>. We present a comprehensive morphological profiling resource using the carefully curated and well-annotated EU-OPENSCREEN Bioactive Compounds. </span><span>The data was generated across four imaging sites with high-throughput confocal microscopes using the </span><span>Hep</span><span> G2 as well as the U2 OS cell line.</span><span> We employed an extensive assay optimization process to achieve high data quality across the different sites. An analysis of the extracted profiles </span><span>validates</span><span> the robustness of the generated data. <span>We used this resource to compare the morphological features of the different cell lines. By correlating the profiles with overall activity, cellular toxicity, several specific mechanisms of action (MOAs), and protein targets, we </span><span>demonstrate</span><span> the dataset's potential for </span><span>facilitating</span><span> more extensive exploration of mechanisms of action.</span> </span></span></p>
Model data for "A model study on investigating the sensitivity of aerosol forcing on the volatilities of semi-volatile organic compounds" by Irfan et al
<p><span>Abstract: </span>This dataset contains simulation results from global aerosol-climate model ECHAM-SALSA. These simulations were performed to study the sensitivity of simulated SOA mass, CCN and radiative forcings to the assumed volatility distributions of biogenic SOA precursor species. The study employed volatility basis set (VBS) approach to represent and simulate SOA in the atmosphere. The study involved a comparative analysis between finely resolved 9-bin VBS setup with a simplified 3-bin VBS setup. It also included how the SOA mass, CCN and radiative forcing are sensitive to the volatitility of individual VBS bins.</p> <p><span>Methods: </span>Global scale aerosol-climate model simulations were performed using ECHAM-SALSA. We performed three diferent simulations each using 9-bin and 3-bin VBS setups with the volatilities increased (VBSx10) and decreased (VBSx0.1) by one-order of magnitude with respect to the original volatility (VBSx1). Another set of six different simuations were performed by increasing and decreasing the volatilities of one VBS bin at a time while keeping the original volatilities of other bins.</p> <p><span>TechnicalInfo: </span>In this study, all the ECHAM-SALSA simulations used T63 spectral truncation and 47 hybrid sigma pressure levels in horizontal and vertical resolution respectively. Simulations were performed for the year 2010 with half a year spin-up. The data was simulated with 3-hourly output for the simulation period. We then calculated monthly means of the summer months from 3-hourly data for all the model values except CDNC. We used the the 3-hourly data to analyse CDNC from grids with cloud fraction ≥ 0.95. A detailed description of model simulations is given in the setup file of each simulation.</p> <p><span>TechnicalInfo: </span>The external URL leads to a bucket containing setup files, the complete dataset (post-processed NETCDF files) presented in the manuscript, and the python scripts used for data analysis for each of the simulations.</p>
The traceability of waste compounds from the orange juice industry by NMR and GC-MS techniques
<p>The traceability of waste compounds from the orange juice industry by NMR and GC-MS techniques</p>
Screening of 6000 compounds for uncoupling activity: input parameters, the predicted uncoupling activity, as well as the results in respect to structural alerts
<p>Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in-vitro uncoupling activity, using a biophysical model based on ab-initio COSMO-RS input parameters with the molecular structure as the only external input. We combined these results with a model for baseline toxicity (narcosis). Our model identified more than 1250 possible uncouplers in the screening dataset, and identified possible new uncoupler classes such as thiophosphoric acids. When tested against 423 known uncouplers and 612 known inactive compounds in the dataset, the model reached a sensitivity of 83% and a specificity of 96%. In a direct comparison, it showed a similar specificity than the structural alert profiler Mitotox (97%), but much higher sensitivity than Mitotox (47%). The biophysical model thus allows for a more accurate screening for uncoupling activity than existing structural alert profilers. We propose to use our model as a complementary tool to screen large datasets for protonophoric uncoupling activity in drug development and toxicity assessment.</p>
The Grammatical Nature of Sino-Vietnamese "Verb-Object Compounds"
<p>This study investigates the grammatical nature of Sino-Vietnamese words borrowed from “verb-object compounds”. I selected 47 verb-object compounds borrowed into Vietnamese as target and investigated whether they maintain their dual identities (i.e., word and phrase) as in Chinese. The results show that functional words cannot be inserted between the constituents of the target words with one exception, and that a number of target words can be followed by an object. Based on the results, I argue that Sino-Vietnamese “verb-object compounds” have almost lost their phrasal identity and that some items have been reinterpreted as transitive verbs.</p>
Virtual screening of the Janssen compound collection against SARS-CoV-2 Mpro
<p>This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Mpro and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Virtual screening of 2629 Janssen compounds against SARS-CoV-2 RdRP
<p>This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Screening of 67 compounds with predicted biosignature profile similar to remdesivir for anti-SARS-CoV-2 activity
<p>This short report describes the most relevant results of screening compounds with a similar predicted biosignature as remdesivir in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Screening of ~7000 coronavirus-specific compounds for anti-SARS-CoV-2 activity
<p>This short report describes the most relevant results of screening selected compounds with potential activity against SARS-CoV-2 in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Comparison of Volatile Flavor Compounds in Plant-based and Real Pork Mince by Headspace-Gas Chromatography-Ion Mo-bility Spectrometry (HS-GC-IMS)
<p>Table S1: The peak intensity of VFCs that identified in six raw pork minces by GC-IMS;</p> <p>Table S2: The peak intensity of VFCs that identified in six steamed pork minces by GC-IMS;</p> <p>Table S3: The peak intensity of VFCs that identified in six stir-fried pork minces by GC-IMS.</p>
Electropherogram data of endogenous compounds in DBS
<p>Electropherogram data (in CSV) and calibration data of the SI-CE-C4D system for endogenous analytes of dried blood spots associated to Fig. 6 of the paper "Automated Sequential Injection-Capillary Electrophoresis for Dried Blood Spot Analysis: A Proof-of-Concept Study" published in Analytical Chemistry, 2022 (10.1021/acs.analchem.1c05130)</p>
Seeds as Potential Sources of Phenolic Compounds and Minerals for Indian population
<p>This is the supplementary information of the paper "Seeds as Potential Sources of Phenolic Compounds and Minerals for Indian population" submitted for publication to the journal "Molecules"</p>
Assessment of compound-specific fatty acid d13C and d2H values to track fish residency and mobility in a small subalpine catchment
<p><span>Methods for identifying origin, movement, and foraging areas of animals are essential for understanding ecosystem connectivity, nutrient flows, and other ecological processes. Telemetric methods can provide detailed spatial coverage but are limited to minimum body size of specimen for tagging. In recent years, stable isotopes have been increasingly used to track animal migration by linking geophysical isotope landscapes called "isoscapes". However, compared to telemetric methods, the spatial resolution of bulk stable isotopes is low.</span></p> <p><span>Here we examined a novel approach by evaluating the use of compound-specific hydrogen and carbon stable isotopes of fatty acids (δ</span><sup><span>2</span></sup><span>H<sub>FA</sub> and </span><span>δ<sup>13</sup></span><span>C<sub>FA</sub>) from liver, muscle, brain, and eye tissues for identifying site-specificity of fish from a sub-alpine river catchment. We analysed 208 fish (European bullhead, rainbow trout, and brown trout) collected in 2016 and 2018 at 15 different sites.</span></p> <p><span>δ<sup>13</sup></span><span>C<sub>FA</sub> values of these fish tissues correlated more amongst each other than those of </span><span><span>δ</span><sup><span>2</span></sup><span>H<sub>FA</sub></span> values. Both </span><span><span>δ</span><sup><span>2</span></sup><span>H<sub>FA</sub></span> and </span><span><span>δ<sup>13</sup></span><span>C<sub>FA</sub></span> values showed tissue-dependent isotopic fractionation, while fish taxa had only small effects. The highest site-specificity was for </span><span>δ<sup>13</sup></span><span>C<sub>DHA</sub> values, while the </span><span>δ<sup>2</sup></span><span>H isotopic difference between LIN and ALA resulted in the highest site-specificity. Using linear discrimination analysis of FA isotope values, over 90 % of fish could be assigned to their location of origin, however, the accuracy dropped to about 56 % when isotope data from 2016 were used to predict the sites for samples collected in 2018, suggesting temporal shifts in site specificity of </span><span><span>δ</span><sup><span>2</span></sup><span>H<sub>FA</sub></span> and </span><span>d</span><span>13</span><span>CFA. However, predictive results were still higher than site specificity compared to bulk tissue isotopes for a single time point. In summary, compound-specific isotope analysis of fatty acids may become a highly effective tool for assessing fine and large-scale movement and foraging areas of animals.</span></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.