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Dataset results
6 results for “CoV2 Spike”
SARS-COV2 Spike Glycopeptide Mass-Retention Time PCDL database
<p>Contains accurate mass, HPLC retention time, peptide sequence, glycan structure and mass spectra for over 400 glycopeptides from elastase digestion of SARS-COV2 Spike antigen and receptor binding domain. The database is used as part of the Mass-Retention Time Fingerprinting method to characterise Spike glycans as described in the BioRxiv preprint “Identification, Mapping and Relative Quantitation of SARS-Cov2 Spike Glycopeptides by Mass-Retention Time Fingerprinting”</p>
SIRAH-CoV2 initiative: Spike D614G mutation (introduced on PDB id:6XR8)
<p>This dataset contains the raw data of a coarse-grained molecular dynamics simulation of the D614G mutant of Spike protein from SARS-CoV-2. The initial coordinates correspond to the PDB structure 6XR8, where the coordinates of the side chain of Aspartate 614 were deleted to produce a Glycine. Missing loops were introduced with Swiss-Model (https://swissmodel.expasy.org). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Glycan parameters correspond to those reported by <a href="http://doi.org/10.1101/2020.12.18.423446">Garay et at.</a>2020. </p> <p>The files spike_D614G_SIRAHcg_rawdata_0-2us.tar, spike_D614G_SIRAHcg_rawdata_2-4us.tar, spike_D614G_SIRAHcg_rawdata_4-6us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file spike_D614G_SIRAHcg_prot_10us.tar contains only the protein coordinates, while spike_D614G_SIRAHcg_prot_10us_skip10ns.tar contains one frame every 10ns. Notice that these two files contain a 10-microsecond trajectory, while the raw data is limited to 6 microseconds because of size restrictions on the database. Raw data from microseconds 6 to 10 is available upon request (see below).</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file spike_D614G_SIRAHcg_prot_10us_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd spike_D614G_SIRAHcg_prot.prmtop spike_D614G_SIRAHcg_prot.ncrst spike_D614G_SIRAHcg_10us_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV-2 initiative.</p> <p>For further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
X-ray diffraction data for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
<p>X-ray diffraction dataset for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) collected at the AMX beamline (17-ID-1) at the National Synchrotron Lightsource II, Brookhaven National Laboratory, Upton, NY, USA.</p> <p>Final XDS.INP file generated by autoPROC.</p> <p>Serialized request document for vector collection from LSDC.</p> <p>KB mirrors</p> <p>Detector: EigerX9M (Si)</p> <p>Approx. photon flux at 13475eV: 4E12 ph/s</p> <p>Approx. beam size: 5 x 7 um</p>
SIRAH-CoV2 initiative: SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
<p>This dataset contains the trajectory of a 3 microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, and 6M17_SIRAHcg_rawdata_2-3.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M17_SIRAHcg_3us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_3us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M17_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_3us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
SIRAH-CoV2 initiative: UPDATED TRAJECTORY of SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
<p>This dataset contains an updated trajectory of a four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). It substitutes the previous one on the same system, which was performed in the absence of disulfide bridges.</p> <p>Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_4usprot_skip.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
SIRAH-CoV2 initiative: S2 Spike core fragment in postfusion state (PDB id:6M1V)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot.ncrst 6M1V_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
ScienceDex guides
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