COVID-19 Data Sets

TRAJECTORIES_INPUTS_DATA_mpro_wt_variants_amarolab.tar.gz -

Developed by the Amaro Lab: TRAJECTORIES_INPUTS_DATA_mpro_wt_variants
positively_bound.ace2_rbd_md_simulations-002.tar.gz-

Developed by the Amaro Lab: positively_bound.ace2_rbd_md_simulations-002.tar.gz
positively_bound.spike_md_simulations-001.tar.gz -

Developed by the Amaro Lab: positively_bound.spike_md_simulations-001.tar.gz
positively_bound.ifd_schrodinger-004.tar.gz -

Developed by the Amaro Lab: positively_bound.spike_md_simulations-001.tar.gz
glycogrip2_files_for_sharing-20230114T015732Z-003.zip -

Developed by the Amaro Lab: glycogrip2_files_for_sharing-20230114T015732Z-003.zip
PSF-PDB_spike_open_prot_glyc_memb_wat_ions_amarolab.tar.gz -

Developed by the Amaro Lab: PSF/PDB for full-length Spike protein in the OPEN state, including protein, glycans, membrane, water and ions.
PSF-PDB_spike_closed_prot_glyc_memb_wat_ions_amarolab.tar.gz -

Developed by the Amaro Lab: PSF/PDB for full-length Spike protein in the CLOSED state, including protein, glycans, membrane, water and ions.
TRAJECTORIES_spike_open_prot_glyc_amarolab.tar.gz -

Developed by the Amaro Lab: Trajectories (PSF + DCDs x 6 replicas) for full-length Spike protein in the OPEN state. Protein + glycans only (not aligned)
TRAJECTORIES_spike_closed_prot_glyc_amarolab.tar.gz -

Developed by the Amaro Lab: Trajectories (PSF + DCDs x 3 replicas) for full-length Spike protein in the CLOSED state. Protein + glycans only (not aligned).
TRAJECTORIES_spike_mutant_prot_glyc_amarolab.tar.gz -

Developed by the Amaro Lab: Trajectories (PSF + DCDs x 6 replicas) for full-length Spike protein in the OPEN state bearing N165A and N234A mutations. Protein + glycans only (not aligned.)
PSF-PDB_ace2_rbd_prot_glyc_memb_wat_ions.amarolab.tar.gz -

Developed by the Amaro Lab: PSF/PDB of ACE2/RBD complex including protein, glycans, membrane, water and ions.
TRAJECTORIES_ace2_rbd_prot_glyc_memb_amarolab.tar.gz -

Developed by the Amaro Lab: Trajectories (PSF + DCDs x 3 replicas) of ACE2/RBD complex. Protein + glycans + membrane (not aligned).
TRAJECTORIES_continuous_spike_opening_WE_chong_and_amarolab.tar.gz -

Developed by Chong and Amaro Labs: Continuous trajectory of spike opening obtained from weighted ensemble simulation. (PSF + PRMTOP + DCD) for spike ectodomain including protein and glycans.
TRAJECTORIES_main_protease_6LU7_mccammon_and_amarolab.tar.gz -

Developed by Amaro and McCammon Labs: Gaussian accelerated MD trajectories (NETCDF + PRMTOP + RST + PDBs x 6 systems x 5 replicates) for main protease. Protein + N3 Ligand (not aligned).
spike_apbs_files_amarolab.tar.gz -

Developed by Amaro Lab
spike_gag_docking_results_amarolab.tar.gz -

Developed by Amaro Lab
nsp14_dry_segname.psf.gz -

NSP14 topology file - Developed by Amaro Lab
trajectories_nsp14_namd_dry_amarolab.dcd.gz -

NSP14 NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
trajectories_nsp14_amber_dry_amarolab.dcd.gz -

NSP14 Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
nsp14_nsp10_dry_segname.psf.gz -

NSP14 + NSP10 topology file - Developed by Amaro Lab
trajectories_nsp14_nsp10_namd_dry_amarolab.dcd.gz -

NSP14 + NSP10 NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
trajectories_nsp14_nsp10_amber_dry_amarolab.dcd.gz -

NSP14 + NSP10 Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
nsp14_rna_dry_segname.psf.gz -

NSP14 + NSP10 + RNA topology file - Developed by Amaro Lab
trajectories_nsp14_nsp10_rna_namd_dry_amarolab.dcd.gz -

NSP14 + NSP10 + RNA NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
trajectories_nsp14_nsp10_rna_amber_dry_amarolab.dcd.gz -

NSP14 + NSP10 + RNA Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab