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Simulation report and files

General information

Name: Fully-glycosylated S protein (head) in closed-closed-closed state in complex with antibody s309

Included proteins: Spike

Uniprot ID: P0DTC2

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6WPS

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: 74904

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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Fully-glycosylated S protein (head) in closed-closed-closed state in complex with antibody s309 ( 6WPS)

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