SARS-CoV-2 (COVID-19) spike protein molecular dynamics simulation data

Published: 14-06-2020| Version 2 | DOI: 10.17632/5hkyvbyctj.2
Contributor:
Elio Cino

Description

Molecular dynamics trajectory data of the SARS-CoV-2 (COVID-19) spike protein. The spike protein is a major target for vaccine development. Datasets include: - 2 x 0.2 µs trajectories of WT prefusion spike protein with site-specific glycans in GROMACS format - 2 x 0.2 µs trajectories of D614G prefusion spike protein with site-specific glycans in GROMACS format - CHARMM-GUI generated GROMACS topologies - GROMACS tpr and checkpoint files for continuing the simulations - Video renderings (protein chains in gray, cyan, and magenta; glycans in yellow) The prefusion spike protein structure used is based on 6VSB (single RBD in the up conformation) with site-specific glycans, see https://www.biorxiv.org/content/10.1101/2020.04.07.030445v1.full. Simulation details: CHARMM36m force field with CHARMM modified TIP3P water model, and 0.15 M NaCl. Equilibration and production (310 K, NPT) were performed with CHARMM-GUI files. *Potential collaborators, please contact eliocino@ufmg.br if you intend to use the data for publication.

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