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28 changes: 28 additions & 0 deletions data/simulations/D-NEMD_spike.yml
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type: md
title: Nonequilibrium simulations of the glycosylated SARS-Cov-2 ancestral spike
description: >
Dynamical nonequilibrium MD (D-NEMD) simulations of the
glycosylated and cleaved at the furin site ectodomain of
the SARS-CoV-2 ancestral spike

creator: A.S.F. Oliveira
organization: University of Bristol
lab: Oliveira and Mulholland Labs
proteins:
- spike
files:
- https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/D-NEMD_glycosylated_spike/D-NEMD_simuls.tar.gz
trajectory:
- https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/D-NEMD_glycosylated_spike/D-NEMD_simuls.tar.gz
structures:
- https://www.rcsb.org/structure/7JJI
size: 8.4 GB
length: 210 D-NEMD replicates, 10 ns each
ensemble: NPT
temperature: 310
pressure: 1
solvent: water
forcefields:
- CHARMM36m
references:
- "Oliveira, ASF et al. “Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike” 2024, eLife (DOI:10.7554/eLife.97313.1)"