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2,489 results for “Sars-CoV-2”
Figure 9 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 9 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 RNA-dependent RNA polymerase (PDB: 7bv2).
Figure 4 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 4 (A) Structure of standard inhibitor of SARS-CoV-2 main protease, N3, (B) 2D pose for the interaction of hydroxychloroquine into the active site of SARS-Cov-2 main protease enzyme.
Figure 8 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 8 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 papain-like protease (PDB: 6wx4).
Figure 10 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 10 The RMSD plot of Coumermycin complex with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, at 50 ns simulation.
Figure 13 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 13 The time frame of evolution against SASA of Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, during 50 ns simulation.
Figure 14 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 14 Protein interaction analysis. The green colour = hydrogen bonding, pink color = ionic interaction, grey colour = hydrophobic interaction and blue colour = water bridges showed in Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp during 50 ns MD simulations.
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 05
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 05 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR. The recorded area shows the profiles of a few ciliated cells which are structurally impaired by vesiculation, probably due to the sampling and storage before fixation. Only few organelles are detectable, including nucleus and some of the mitochondria. The cells are surrounded by cellular debris and heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus particles are not visible.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Supplemental files for Immuno-microbial signature of vaccine-induced immunity of SARS-CoV-2
<p>Supplemental files for Immuno-microbial signature of vaccine-induced immunity of SARS-CoV-2 </p>
Figure S1: SARS-CoV-2-specific neutralization activity at days 1 and 8 relative to enrollment in exposed seronegative nasal SIgA positive and infected participants.
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Data and code for "SARS-CoV-2 correlates of protection from infection against variants of concern"
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Computational Evidence for Bisartan Arginine Blockers as Next-Generation Pan-Antiviral Therapeutics Targeting SARS-CoV-2, Influenza, and Respiratory Syncytial Viruses (RawData)
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AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
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Database of Study SARS-CoV-2 Antibody Level after Homologous and Heterologous Booster Vaccines an 18-month Longitudinal Observational Cohort Study in Indonesia (Ardyanto et el., 2024)
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Characterization of Neutrophil Functional Responses to SARS-CoV-2 Infection in a Translational Feline Model for COVID-19
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Machine Learning on the Impacts of Mutations in the SARS-CoV-2 Spike RBD on Binding Affinity to Human ACE2 based on Deep Mutational Scanning Data
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Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing
<p><b>Introduction</b>: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. <span>Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited</span>. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing.</p> <p><b>Methods</b>: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using <i>RdRP</i> and <i>N1</i> gene targets in NPS and saliva respectively.</p> <p><b>Results</b>: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample (<i>p</i>=0.860). A highly significant correlation (r = 0.475, <i>p</i><0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens.</p> <p><b>Conclusions</b>: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Less invasive and accurate saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.</p>
Data from: Immunoreactive peptide maps of SARS-CoV-2
<p>Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity among the human coronaviruses (HCoVs) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. To study humoral immune responses specific to SARS-CoV-2, it is imperative to identify peptides that may enable discrimination between exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide microarray and plasma samples collected at two time points from 50 subjects with SARS-CoV-2 infection confirmed by qPCR, samples collected in 2004-2005 from 11 subjects with IgG antibodies to SARS-CoV-1, 11 subjects with IgG antibodies to other seasonal human coronaviruses (HCoV), and 10 healthy human subjects. The peptide microarrays consist of ~172000 12-mer peptide probes spanning whole viral genomes. This dataset consists of reactivity values for individual peptides from all 132 plasma samples for both IgG and IgM. Also made available is the correspondence key that provides a reference for all viral genome sequences that a peptide originated from.</p>
FASTA sequences of 6 different proteins of SARS-CoV-2
<p>The acute respiratory disease induced by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The virulence of the SARS-CoV-2 is mostly regulated by its proteins but very little is known about the protein structures and functionalities. Therefore, the main purpose of this study is to learn more about these proteins through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein have been selected from a Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools and strategies were implemented for multiple sequence alignment and phylogeny analysis with 9 different variants, predicting hydropathicity, amino acid compositions, protein-binding propensity, protein disorders, 2D and 3D protein modeling.</p>
Figure 5 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 5 Analysis of the conformation and interaction of hydrogen bonds between ligands and receptors with a distance < 5 Å. A. ACE-2-ptilidepsin; B. PLpro -ptilidepsin; C. Mpro-ptilidepsin.
Figure 4 from: Syahputra G, Gustini N, Bustanussalam B, Hapsari Y, Sari M, Ardiansyah A, Bayu A, Putra MY (2021) Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors. Pharmacia 68(3): 533-560. https://doi.org/10.3897/pharmacia.68.e68432
Figure 4 Analysis of the conformation and interaction of hydrogen bonds between ligands and receptors with a distance < 5 Å. A. ACE-2-dieckol; B. PLpro -dieckol; C. Mpro-dieckol.
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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.