Repository of molecular dynamics simulations

605 simulations

Engine: GROMACS

Dynarepo 4X33
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
PPIs from test53, Classical MD simulations, 3 replicates of 500 ns
Open
PDB 4X33Published 10 Jul 2025
Dynarepo 4V0O
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
PPIs from test53, Classical MD simulations, 3 replicates of 500 ns
Open
PDB 4V0OPublished 10 Jul 2025
Dynarepo 4M0W
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
PPIs from test53, Classical MD simulations, 3 replicates of 500 ns
Open
PDB 4M0WPublished 10 Jul 2025
Dynarepo 4LVN
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
PPIs from test53, Classical MD simulations, 3 replicates of 500 ns
Open
PDB 4LVNPublished 10 Jul 2025
Dynarepo 4FZV
Omid Mokhtari, Hamed Khakzad, Yasaman Karami
PPIs from test53, Classical MD simulations, 3 replicates of 500 ns
Open
PDB 4FZVPublished 9 Jul 2025
SARS-CoV-2 RBD and Human ACE2 complex
Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero, et al.
COVID-19 MD simulation without water residues
Open
PDB 6M0JCC BY 4.0Published 17 Jul 2023
BANAL-52-103-CoV RBD and Human ACE2 complex
Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero, et al.
COVID-19 MD simulation without water residues
Open
No structureCC BY 4.0Published 17 Jul 2023
BANAL-236-CoV RBD and Human ACE2 complex
Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero, et al.
COVID-19 MD simulation without water residues
Open
No structureCC BY 4.0Published 17 Jul 2023
Folding@home simulations of the SARS-CoV-2 spike protein
Maxwell I. Zimmerman
Markov state model built from 1.2 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 6VXXCC BY 4.0Published 16 Feb 2023
Folding@home simulations of the nucleoprotein monomer
Maxwell I. Zimmerman
Markov state model built from aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
No structureCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nucleoprotein DD dimer
Maxwell I. Zimmerman
Markov state model built from aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
No structureCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp9
Maxwell I. Zimmerman
Markov state model built from 9 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 6W4BCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp8
Maxwell I. Zimmerman
Markov state model built from 1.8 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 2AHMCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp7
Maxwell I. Zimmerman
Markov state model built from 3.7 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 5F22CC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp5 monomer
Maxwell I. Zimmerman
Markov state model built from 6.4 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 6Y2ECC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp5 dimer
Maxwell I. Zimmerman
Markov state model built from 2.9 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 6Y2ECC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp3 pl2pro domain
Maxwell I. Zimmerman
Markov state model built from 731 microseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 3E9SCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp3 macrodomain complex
Maxwell I. Zimmerman
Markov state model built from 11 miliseconds of aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
PDB 6W02CC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp16
Maxwell I. Zimmerman
Markov state model built from aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
No structureCC BY 4.0Published 15 Feb 2023
Folding@home simulations of nsp15
Maxwell I. Zimmerman
Markov state model built from aggregate simulation time collected on Folding@home. Folding@home simulations were launched from the structures generated using an adaptive sampling method (FAST-Pocket).
Open
No structureCC BY 4.0Published 15 Feb 2023