Find research datasets worth reusing

Raw diffraction data for structure of SARS-CoV-2 main protease with Z31432226 (ID: mpro-x0376 / PDB: 5REA)

Raw diffraction data for mpro-x0376 / PDB ID 5REA (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REA) - SARS-CoV-2 main protease in complex with Z31432226 (SMILES:O=C(N1CCCCCC1)C=2C=CC=3OCOC3C2) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

Raw diffraction data for structure of SARS-CoV-2 main protease with Z1129283193 (ID: mpro-x0107 / PDB: 5RE4)

Raw diffraction data for mpro-x0107 / PDB ID 5RE4 (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RE4) - SARS-CoV-2 main protease in complex with Z1129283193 (SMILES:CC(=O)NC=1C=NC=CC1C) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

Raw diffraction data for structure of SARS-CoV-2 main protease with Z2737076969 (ID: mpro-x0350 / PDB: 5RE8)

Raw diffraction data for mpro-x0350 / PDB ID 5RE8 (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RE8) - SARS-CoV-2 main protease in complex with Z2737076969 (SMILES:FC=1C=CC=C(CNCC2=CC=CO2)C1) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

Raw diffraction data for structure of SARS-CoV-2 main protease with Z45617795 (ID: mpro-x0072 / PDB: 5R7Y)

Raw diffraction data for mpro-x0072 / PDB ID 5R7Y (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5R7Y) - SARS-CoV-2 main protease in complex with Z45617795 (SMILES:CS(=O)(=O)NCCC=1C=CC=CC1) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

Raw diffraction data for structure of SARS-CoV-2 main protease with Z1220452176 (ID: mpro-x0104 / PDB: 5R7Z)

Raw diffraction data for mpro-x0104 / PDB ID 5R7Z (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5R7Z) - SARS-CoV-2 main protease in complex with Z1220452176 (SMILES:CC(=O)NCCC1=CNC=2C=CC(F)=CC12) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

Raw diffraction data for structure of SARS-CoV-2 main protease with Z979145504 (ID: mpro-x1235 / PDB: 5RFC)

Raw diffraction data for mpro-x1235 / PDB ID 5RFC (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFC) - SARS-CoV-2 main protease in complex with Z979145504 (SMILES:COC(=O)NC=1SC(C)=NC1C=2C=CC=CC2) collected as part of an XChem crystallographic fragment screening campaign on beamline i04-1 at Diamond Light Source. The deposited structure was automatically processed with standard Diamond tools and PanDDA, however the raw data are being made available to allow reanalysis by any interested party. For more details see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html

opencc-by-4.0Mar 2020View details →

Training data for 'Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads' tutorial (Galaxy Training Material)

The data here is a copy of the corresponding SRR records in the NCBI SRA. The duplication serves a dual purpose: <ol> <li>as a backup should there be problems connecting to NCBI servers, e.g., during Galaxy user trainings.</li> <li>to illustrate how to obtain raw sequencing data from alternative sources, and to organize the data into the same collection structure in a Galaxy history that is generated by specialized Galaxy SRA download tools.</li> </ol>

opencc-by-4.0Apr 2020View details →

The airborne lifetime of small speech droplets and their potential importance to SARS-CoV-2 transmission

Movies that show the experimental setup and the full 85-minute observation of speech droplet nuclei.   The full movie recording of highly sensitive laser light scattering observations that indicate loud-speaking generates, in addition to hundreds of regular droplets, also many thousands of micro-droplets per second. This movie clip shows the decay of airborne particles.   Note: some parts of the audio of the clips were muted for privacy.

Haruspex Analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 pdb entry 7bv1 emdb 30209

Haruspex (version 1.0 190116) analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 , pdb entry 7bv1 , emdb 30209. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421

Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6m17 emdb 30039

Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6m17 , emdb 30039. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421

Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6vsj emdb 21377

Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6vsj , emdb 21377. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421

Haruspex Analysis for SARS-CoV-2 surface_glycoprotein pdb entry 6vsb emdb 21375

Haruspex (version 1.0 190116) analysis for SARS-CoV-2 surface_glycoprotein , pdb entry 6vsb , emdb 21375. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421

Haruspex Analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 pdb entry 6m71 emdb 30127

Haruspex (version 1.0 190116) analysis for SARS-CoV-2 rna_polymerase-nsp7-nsp8 , pdb entry 6m71 , emdb 30127. https://onlinelibrary.wiley.com/doi/10.1002/anie.202000421

Investigating evolution at the catalytic site of the main SARS-CoV-2 protease using over 15,000 genomes

We investigated evolution and genomic variation of SARS-CoV-2 within the current pandemic at the catalytic site of the main SARS-CoV-2 protease (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and <a href="https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/">https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ </a>). We used more than 15,000 genomic sequences from GISAID (<a href="https://www.epicov.org/">https://www.epicov.org/</a>) available on the 17th of May 2020. We use a new approach based on phylogenetic inference of homoplasy, clustering of mutations, and ambiguous consensus sequence characters, to identify sites that are likely affected by sequencing artefacts. We find that these sites are mostly conserved, and the amino acid variants observed are only M49I, P52S, N142S, and P168S, all of which appear only at extremely low frequencies (maximum of two samples each).

opencc-by-4.0Jun 2020View details →

Datasets for GTN tutorial on SARS-CoV-2 variant analysis

A reference genome in FASTA format is provided for SARS-CoV-2, "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", having the accession ID of NC_045512.2. This file was obtained from NCBI within this Galaxy history: https://usegalaxy.org/u/dan/h/nc0455122-from-ncbi

opencc-by-4.0Jun 2020View details →

QM/MM MD simulations of the ES complexes of SARS-CoV-2 main protease and oligopeptide substrates

qmdcd.7z : QM/MM MD trajectories for all considered systems in dcd format for QM parts without link atoms (QMpart_nolink.pdb) frames.7z : QM parts of the MD frames selected for the electron density analysis.

openother-openJul 2020View details →

ekoraytascilar/naturecommunicationscovid: Data and analysis code to accompany "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"

This release contains raw datasets and analysis code for the research paper titled "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"

opencc-by-4.0Jul 2020View details →

SARS-CoV-2 detection dogs - a pilot study

The outstanding olfactory acuity of canines led us to consider whether dogs are able to reliably detect the odour of respiratory diseases associated with a SARS-CoV-2 infection in saliva or tracheobronchial secretion of hospitalized COVID-19 patients. Furthermore, we examined if SARS-CoV-2 detection dogs could provide an appropriate screening method for the human virus.The aim of this data publication is to provide the data acquired in the controlled, randomized and double-blinded pilot study `Scent dog identification of SARS-CoV-2 infection’ (submitted to BMC Infectious Diseases).

dryad36/100

On the evolutionary epidemiology of SARS-CoV-2

There is no doubt that the novel coronavirus SARS-CoV-2 that causes COVID-19 is mutating and thus has the potential to adapt during the current pandemic. Whether this evolution will lead to changes in the transmission, the duration, or the severity of the disease is not clear. This has led to considerable scientific and media debate, from raising alarms about evolutionary change to dismissing it. Here we review what little is currently known about the evolution of SARS-CoV-2 and extend existing evolutionary theory to consider how this disease might evolve during the COVID-19 pandemic. While there is currently no definitive evidence that SARS-CoV-2 is undergoing further adaptation, continued, evidence-based, analysis of evolutionary change is important so that public health measures can be adjusted in response to substantive changes in the infectivity or severity of COVID-19.

opencc-zeroDec 2019View details →