Digital Object Identifier (DOI)
List of DOIs issued by MolSSI
Apo SARS-CoV PLPro
DOI: 10.34974/5x0s-wa16
Description: 1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.
Purpose: SARS-CoV MD Trajectory
Creator: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Owner: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Size: 5.4 GB
Content:
PLpro 1μs MD trajectory
Topology file
File types: dcd prmtop
3k Bound SARS-CoV PLPro
DOI: 10.34974/67wv-1d18
Description: 1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped of water molecules and counter ions.
Purpose: SARS-CoV MD Trajectory
Creator: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Owner: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Size: 5.5 GB
Content:
PLpro 1μs MD trajectory
Topology file
File types: dcd prmtop
Apo SARS-CoV-2 PLPro (From PDB 6W9C C-Chain)
DOI: 10.34974/y5f0-0k68
Description: 1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.
Purpose: SARS-CoV-2 MD Trajectory
Creator: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Owner: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Size: 5.5 GB
Content:
PLpro 1μs MD trajectory
Topology file
File types: dcd prmtop
3k Bound SARS-CoV-2 PLPro (3k Docked to Frame From Trajectory of PDB 6W9C C-Chain)
DOI: 10.34974/mawv-qh58
Description: 1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped of water molecules and counter ions.
Purpose: SARS-CoV-2 MD Trajectory
Creator: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Owner: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Size: 5.5 GB
Content:
PLpro 1μs MD trajectory
Topology file
File types: dcd prmtop
Apo SARS-CoV-2 PLPro (From PDB 6WRH C-Chain)
DOI: 10.34974/wrvg-v570
Description: 1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.
Purpose: SARS-CoV-2 MD Trajectory
Creator: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Owner: Chia-en A. Chang, Yuliana Bosken & Timothy Cholko
Size: 5.5 GB
Content:
PLpro 1μs MD trajectory
Topology file
File types: dcd prmtop
ANI-FDA Drugs Archive
DOI: 10.34974/wjn9-bs39
Description: The dataset files contain low-energy conformers and tautomers of 6,433 FDA approved & investigational drugs. A collection consists of 32,036 tautomeric structures and ~3M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges.
Purpose: Data for tautomers And conformers Of 6,433 FDA approved investigational drugs published in 2020
Creator: Olexandr Isayev
Owner: Olexandr Isayev
Size: 2.1 GB
Content:
Conformer total energy
Conformer relative energy
Conformer dipole-consistent partial atomic charges
File types: sdf
Files: [.]
License: CC BY-NC-ND 4.0
ANI-CAS Antiviral Archive
DOI: 10.34974/hyp8-pb26
Description: The dataset files contain low-energy conformers and tautomers for 20,306 from the CAS Antiviral database. Original ~50K molecules were filtered for duplicates and drug-likeness. A collection consists of 67,167 tautomeric structures and ~6.6M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges.
Purpose: Data for automers and conformers from the CAS antiviral database published in 2020
Creator: Olexandr Isayev
Owner: Olexandr Isayev
Size: 5.3 GB
Content:
Conformer total energy
Conformer relative energy
Conformer dipole-consistent partial atomic charges
File types: sdf
Files: [.]
License: CC BY-NC-ND 4.0
GREST_SSCR Simulation of Trimeric SARS-CoV-2 Spike Protein Starting From Down Conformation
DOI: 10.34974/wtbx-0r84
Description: Trimetric SARS-CoV-2 spike glycoprotein in the Down State with and without simulation box, and with and without glycan. Provided by the Sugita Lab of RIKEN
Purpose: Clustering simulation data for the spike glycoprotein starting in the down state.
Creator: Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, and Yuji Sugita
Owner: RIKEN and the Sugita Lab
Size: ~250 MB, split evenly over files
Content:
Models of the glygoprotein and simulation clustering ensembles
File types: PSF/PDB models PDB Trajectories
Files: [.] [.] [.] [.] [.] [.] [.] [.]
GREST_SSCR Simulation of Trimeric SARS-CoV-2 Spike Protein Starting From 1Up Conformation
DOI: 10.34974/xn67-xk26
Description: Trimetric SARS-CoV-2 spike glycoprotein in the 1Up State with and without simulation box, and with and without glycan. Provided by the Sugita Lab of RIKEN
Purpose: Clustering simulation data for the spike glycoprotein starting in the 1Up state.
Creator: Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, and Yuji Sugita
Owner: RIKEN and the Sugita Lab
Size: ~150 MB, split evenly over files
Content:
Models of the glygoprotein and simulation clustering ensembles
File types: PSF/PDB models PDB Trajectories
Files: [.] [.] [.] [.] [.] [.]
SARS-COV-2 Coarse Grained Viron Model
DOI: 10.34974/q8ya-wh69
Description: A coarse-grained (CG) model for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to Gregory A Voth in response to the COVID-19 pandemic.
Purpose: Coarse-grained structural data for the SARS-CoV-2 virion
Creator: Alvin Yu & Gregory Voth
Owner: Alvin Yu & Gregory Voth
Size: 17.3 MB
Content:
Coarse-grained structure of SARS-CoV-2 virion
File types: pdb
Files: [.]
Multiscale Models for the SARS-CoV-2 Virion
DOI: 10.34974/j0v0-3d76
Description: A coarse-grained (CG) model for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to Gregory A Voth in response to the COVID-19 pandemic.
Purpose: Coarse-grained data for multiscale models of the SARS-CoV-2 virion
Creator: Alvin Yu & Gregory Voth
Owner: Alvin Yu & Gregory Voth
Size: 6.2 MB
Content:
Coarse-grained structural data for the for the SARS-CoV-2 virion
File types: pdb
Files: [.]