Folding@home simulations of nsp8

Open

Maxwell I. Zimmerman;

MD-A001UQ

Created: 15 Feb 2023
License: This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License (opens in a new tab)

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).

Molecular system

Starting structure: 2AHMPDB 2AHM(opens in a new tab)
Force field: Amber ff03TIP3P
Engine: GROMACS 5.0.4
Method: Markov state model (MSM)
Ensemble: NPT
Temperature: 300 K
Timestep: 4 fs
Frames: 10,000
Composition: Molecules of interest
NSP8Protein · 1 chain2,977 atoms191 residues
Total2,977 atoms191 residues
Box dimensions: Dodecahedron

Sequences

Sequence 1Protein · 191 residues

IASEFSSLPS YAAFATAQEA YEQAVANGDS EVVLKKLKKS LNVAKSEFDR DAAMQRKLEK MADQAMTQMY KQARSEDKRA KVTSAMQTML FTMLRKLDND ALNNIINNAR DGCVPLNIIP LTTAAKLMVV IPDYNTYKNT CDGTTFTYAS ALWEIQQVVD ADSKIVQLSE ISMDNSPNLA WPLIVTALRA N

Run	Outputs
replica 1	Trajectory Analyses

Files

42 files · 454 MB

All files454 MB

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Acknowledgements

We are grateful to the citizen scientists who contribute to Folding@home by running simulations on their personal computers.

Folding@home simulations of nsp8

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements