Developed by the Amaro Lab: md_pro
Developed by the Amaro Lab: D614G_FOR_SHARING_amarolab.tar.gz
Developed by the Amaro Lab: D614G_FOR_SHARING_amarolab_inputs_routes.tar.gz
Developed by the Amaro Lab: TRAJECTORIES_INPUTS_DATA_mucins_breaking_down_bottlebrush_amarolab.tar.gz
Developed by the Amaro Lab: HexaPro-SS_S2_cMD_GaMD_WE_FEC_simulation_data-- Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens. Input files and trajectories for conventional MD,GaMD, WE MD simulations, and free energy calculations.
Developed by the Amaro Lab: TRAJECTORIES_INPUTS_DATA_mpro_wt_variants
Developed by the Amaro Lab: positively_bound.ace2_rbd_md_simulations-002.tar.gz
Developed by the Amaro Lab: positively_bound.spike_md_simulations-001.tar.gz
Developed by the Amaro Lab: positively_bound.spike_md_simulations-001.tar.gz
Developed by the Amaro Lab: glycogrip2_files_for_sharing-20230114T015732Z-003.zip
Developed by the Amaro Lab: PSF/PDB for full-length Spike protein in the OPEN state, including protein, glycans, membrane, water and ions.
Developed by the Amaro Lab: PSF/PDB for full-length Spike protein in the CLOSED state, including protein, glycans, membrane, water and ions.
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)
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).
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.)
Developed by the Amaro Lab: PSF/PDB of ACE2/RBD complex including protein, glycans, membrane, water and ions.
Developed by the Amaro Lab: Trajectories (PSF + DCDs x 3 replicas) of ACE2/RBD complex. Protein + glycans + membrane (not aligned).
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.
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).
Developed by Amaro Lab
Developed by Amaro Lab
NSP14 topology file - Developed by Amaro Lab
NSP14 NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
NSP14 Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
NSP14 + NSP10 topology file - Developed by Amaro Lab
NSP14 + NSP10 NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
NSP14 + NSP10 Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
NSP14 + NSP10 + RNA topology file - Developed by Amaro Lab
NSP14 + NSP10 + RNA NAMD Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
NSP14 + NSP10 + RNA Amber Trajectories (3 MD replicas concatanated) - Developed by Amaro Lab
Developed by the Amaro Lab: HIV-1_Env_BG505_Full-Length_MD_simulation_dataset This archive contains the equilibrated structures and production molecular dynamics trajectories for the full-length HIV-1 Env systems.
Developed by the Amaro Lab: This archive contains the corresponding model PDB structures used for the simulations.
Developed by the Amaro Lab: Topology and coordinate files (PSF/PDB/JS) extracted from the last frame of all-atom, whole-virion MD simulation of Influenza A/45/Michigan/2015(H1N1). Only protein, glycans, and lipids are included.
Developed by the Amaro Lab: Full trajectory (DCD) of all-atom, whole-virion MD simulation of Influenza A/45/Michigan/2015(H1N1). Only protein, glycans, and lipids are included (no hydrogens). Load on top of the respective PSF file.
Developed by the Amaro Lab: Topology and coordinate files (PSF/PDB/JS) extracted from the last frame of all-atom, whole-virion MD simulation of Influenza A/swine/N1/Shandong/2009(H1N1). Only protein, glycans, and lipids are included.
Developed by the Amaro Lab: Full trajectory (DCD) of all-atom, whole-virion MD simulation of Influenza A/swine/N1/Shandong/2009(H1N1). Only protein, glycans, and lipids are included (no hydrogens). Load on top of the respective PSF file.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: These archives contain the initial structure, final structure, and equilibration trajectory of the following systems:, Synaptic vesicle, Plasma membrane, Endosome membrane, Exosome membrane, Mitochondria-derived vesicle, and HIV-1 membrane.
Developed by the Amaro Lab: Data of the article titled “Dynamic Profile of DNA-bound Full-length p53 Tetramer
Developed by the Amaro Lab: Data of the article titled: Regulatory interactions between APOBEC3B N- and C-terminal domains
Developed by the Amaro Lab: Human Cytosolic Phospholipase A2 and membrane MD simulations