Workbench
General information
Name: Fully-glycosylated S protein (head) in open-open-closed state in complex with antibody c002
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 7K8U
Submitted by: Lehigh University, Bethlehem (CHARMM-GUI)
Submission date: May 20, 2021
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 75069
Simulation details
Software and version: GROMACS 2018.6
Forcefield and version: CHARMM36(m) -
Time step : 4.0 fs
Delta : 1.0 ns
Replicates: 1
Accumulated simulation time: 0.5210 µs
References
Cao, Y.; Choi, Y.K.; Frank, M.; Woo, H.; Park, S.-J.; Yeom, M.S.; Seok, C.; Im, W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. bioRxiv 2021, 2021.05.10.443519. DOI: 10.1101/2021.05.10.443519
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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.
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