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.
85
datasets available to search
ShareScore release 0.9.0
Dataset results
85 results for “SARS CoV 2 Mpro”
Molecular dynamics trajectories for SARS-CoV-2 Mpro with 7 HIV inhibitors
<p>Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir) were calculated on massively parallel supercomputer HOKUSAI Big Waterfall at RIKEN ISC, and a special-purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. For each ligand, 200ns length 28 trajectories were calculated. Some of these trajectories were calculated further longer. We can observe formation of encounter complex and investigate potential binding sites on the surface of the dimeric protease. We hope that these raw data are valuable for further drug repurposing/development research targeting the SARS-CoV-2 main protease. We will submit analysis of these data to refereed journal.</p> <p>Molecular dynamics simulations were performed under NVT at 310K, with the time step 2.5fs. The starting structure was prepared based on PDB 6LU7, with amber14sb force field in about 10nm cubic box with periodic boundary conditions. The ligands were initially placed apart from the active sites of the dimeric main protease.</p> <p>We have also already deposited 10 microseconds trajectories of the dimeric protease without ligand (with amber99sb-ildn force field) in the repository https://data.mendeley.com/datasets/vpps4vhryg/1 (DOI:10.17632/vpps4vhryg.1).</p> <p>Files:</p> <ul> <li><strong><em>LIG</em></strong>_28traj200ns_every200ps.zip (28trajectories for each ligand) <ul> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/<strong><em>a</em></strong>/traj200ns_every200ps_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>(trajectory in GROMACS XTC)</li> </ul> </li> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/<strong><em>a</em></strong>/conf.gro <ul> <li>(initial condition in GROMACS GRO)</li> </ul> </li> <li>traj200ns_every200ps/<em><strong>LIG</strong></em>/topology/ <ul> <li>(contains topology files)</li> </ul> </li> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/mdp/ <ul> <li>(contains run paramter files)</li> </ul> </li> </ul> </li> <li>ZZZ_20traj1us_every200ps.zip (20trajectories extended to 1microsecond) <ul> <li>traj1us_every200ps/traj1us_every200ps_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>DAR-C-06, DAR-D-07</li> <li>IND-C-05, IND-C-06, IND-D-06</li> <li>LOP-A-02, LOP-D-03</li> <li>NEL-B-01, NEL-C-07, NEL-D-02</li> <li>RIT-B-07, RIT-C-07</li> <li>SAQ-B-01, SAQ-C-04, SAQ-D-03</li> <li>TPR-A-07, TPR-B-04, TPR-B-06, TPR-C-05, TPR-D-02</li> </ul> </li> </ul> </li> <li>ZZZ_3traj6us_every1ns.zip (3trajectories extended to 6microseconds or more) <ul> <li>traj6us_every1ns/traj6us_every1ns_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>IND-D-06, NEL-B-01, TPR-B-04</li> </ul> </li> </ul> </li> </ul> <p> </p> <ul> <li>ZZZ_LigandBindingPosePDBs.zip (pickup 3 snapshots for each ligand) <ul> <li>LigandBindingPosePDBs/<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_frame.pdb</li> </ul> </li> </ul> <p> </p> <ul> <li>movies_overlooking_28traj200ns.zip (7x2movies) <ul> <li>movies_28traj200ns/movie_overlooking_<strong><em>LIG</em></strong>_28traj200ns-viewA.mp4 <ul> <li>inspecting 28traj at once</li> </ul> </li> <li>movies_28traj200ns/movie_overlooking_<strong><em>LIG</em></strong>_28traj200ns-viewB.mp4 <ul> <li>from the opposite angle</li> </ul> </li> </ul> </li> <li>movies_1us.zip (17movies) <ul> <li>movies_1us/movie_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_1us.mp4</li> </ul> </li> <li>movies_6us.zip (3movies) <ul> <li>movies_6us/movie_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_6us.mp4</li> </ul> </li> </ul> <p> where</p> <p> <em><strong>LIG</strong></em>={DAR,IND,LOP,NEL,RIT,SAQ,TPR}<br> DAR:darunavir<br> IND:indinavir<br> NEL:nelfinavir<br> RIT:ritonavir<br> SAQ:saquinavir<br> TPR:tipranavir<br> <em><strong>a</strong></em>={A,B,C,D}<br> <em><strong>n</strong></em>={01,02,03,04,05,06,07}</p> <p> </p> <ul> <li>ZZZz_3traj1us_every200ps_unbinding.zip (3trajectories extended to 1microsecond exhibiting unbinding)</li> <li>ZZZz_56traj200ns_every200ps_negative_control.zip (56trajectories as a negative control)</li> <li>ZZZz_LigandBindingPosePDBsRevised.zip (pickuped 3 snapshots for each ligand)</li> </ul> <p> </p>
Raw diffraction data for structure of SARS-CoV-2 main protease with PCM-0102974 (ID: mpro-x1458 / PDB: 5RFY)
Raw diffraction data for mpro-x1458 / PDB ID 5RFY (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFY) - SARS-CoV-2 main protease in complex with PCM-0102974 (SMILES:CC(C)N(C)C(=O)C1CCN(CC1)C(=O)CCl) 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 PCM-0102254 (ID: mpro-x1425 / PDB: 5RFX)
Raw diffraction data for mpro-x1425 / PDB ID 5RFX (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFX) - SARS-CoV-2 main protease in complex with PCM-0102254 (SMILES:COc1ccc(cc1)N2CCN(CC2)C(=O)CCl) 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 PCM-0102121 (ID: mpro-x1402 / PDB: 5RFU)
Raw diffraction data for mpro-x1402 / PDB ID 5RFU (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFU) - SARS-CoV-2 main protease in complex with PCM-0102121 (SMILES:ClCC(=O)N1CCN(CC1)S(=O)(=O)c2ccc(Cl)s2) 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 PCM-0102432 (ID: mpro-x1392 / PDB: 5RFT)
Raw diffraction data for mpro-x1392 / PDB ID 5RFT (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFT) - SARS-CoV-2 main protease in complex with PCM-0102432 (SMILES:ClCC(=O)N1CC(c2ccccc2)c3ccccc3C1) 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 PCM-0102169 (ID: mpro-x1385 / PDB: 5RFR)
Raw diffraction data for mpro-x1385 / PDB ID 5RFR (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFR) - SARS-CoV-2 main protease in complex with PCM-0102169 (SMILES:ClCC(=O)N1CCN(Cc2ccc(Br)s2)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 PCM-0102868 (ID: mpro-x1375 / PDB: 5RFN)
Raw diffraction data for mpro-x1375 / PDB ID 5RFN (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFN) - SARS-CoV-2 main protease in complex with PCM-0102868 (SMILES:Fc1ccc(cc1)N(C2CS(=O)(=O)C=C2)C(=O)CCl) 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 PCM-0102190 (ID: mpro-x1382 / PDB: 5RFP)
Raw diffraction data for mpro-x1382 / PDB ID 5RFP (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFP) - SARS-CoV-2 main protease in complex with PCM-0102190 (SMILES:CC(NC(=O)CCl)c1cccc(Cl)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 PCM-0102179 (ID: mpro-x1384 / PDB: 5RFQ)
Raw diffraction data for mpro-x1384 / PDB ID 5RFQ (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFQ) - SARS-CoV-2 main protease in complex with PCM-0102179 (SMILES:ClCC(=O)Nc1cccc(c1)N2CCCC2=O) 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 PCM-0102972 (ID: mpro-x1380 / PDB: 5RFO)
Raw diffraction data for mpro-x1380 / PDB ID 5RFO (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFO) - SARS-CoV-2 main protease in complex with PCM-0102972 (SMILES:ClCC(=O)N1CCC(CC1)C(=O)N2CCCCC2) 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 Z509756472 (ID: mpro-x1249 / PDB: 5RFE)
Raw diffraction data for mpro-x1249 / PDB ID 5RFE (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RFE) - SARS-CoV-2 main protease in complex with Z509756472 (SMILES:O=C(NCC=1C=CC(C#N)=CC1)N2CCOCC2) 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 NCL-00024905 (ID: mpro-x0967 / PDB: 5RG1)
Raw diffraction data for mpro-x0967 / PDB ID 5RG1 (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RG1) - SARS-CoV-2 main protease in complex with NCL-00024905 (SMILES:CC(=O)NC(Cc1ccc(cc1)O)C(=O)NCC#CBr) 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 NCL-00023830 (ID: mpro-x0946 / PDB: 5RF1)
Raw diffraction data for mpro-x0946 / PDB ID 5RF1 (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RF1) - SARS-CoV-2 main protease in complex with NCL-00023830 (SMILES:BrC1=CC=C(S(N)(=O)=O)C=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 POB0129 (ID: mpro-x0874 / PDB: 5REZ)
Raw diffraction data for mpro-x0874 / PDB ID 5REZ (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REZ) - SARS-CoV-2 main protease in complex with POB0129 (SMILES:O=C([C@@H]1[C@H](C2=CSC=C2)CCC1)N) 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 PCM-0103016 (ID: mpro-x0734 / PDB: 5REM)
Raw diffraction data for mpro-x0734 / PDB ID 5REM (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REM) - SARS-CoV-2 main protease in complex with PCM-0103016 (SMILES:[O-][N+](=O)c1ccccc1N2CCN(CC2)C(=O)CCl) 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 PCM-0102241 (ID: mpro-x0689 / PDB: 5REJ)
Raw diffraction data for mpro-x0689 / PDB ID 5REJ (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REJ) - SARS-CoV-2 main protease in complex with PCM-0102241 (SMILES:ClCC(=O)N1CCN(CC1)S(=O)(=O)c2cccs2) 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 PCM-0102275 (ID: mpro-x0820 / PDB: 5REW)
Raw diffraction data for mpro-x0820 / PDB ID 5REW (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REW) - SARS-CoV-2 main protease in complex with PCM-0102275 (SMILES:CC(NC(=O)CCl)c1cccc2ccccc12) 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 PCM-0102425 (ID: mpro-x0749 / PDB: 5REN)
Raw diffraction data for mpro-x0749 / PDB ID 5REN (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REN) - SARS-CoV-2 main protease in complex with PCM-0102425 (SMILES:ClCC(=O)N1CCCC(C1)c2nc3ccccc3s2) 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 PCM-0102615 (ID: mpro-x0759 / PDB: 5RER)
Raw diffraction data for mpro-x0759 / PDB ID 5RER (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5RER) - SARS-CoV-2 main protease in complex with PCM-0102615 (SMILES:Fc1ccc(cc1)C2CN(CCO2)C(=O)CCl) 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 PCM-0102201 (ID: mpro-x0755 / PDB: 5REP)
Raw diffraction data for mpro-x0755 / PDB ID 5REP (see: https://www.ebi.ac.uk/pdbe/entry/pdb/5REP) - SARS-CoV-2 main protease in complex with PCM-0102201 (SMILES:Fc1cccc(F)c1S(=O)(=O)N2CCN(CC2)C(=O)CCl) 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
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.