Folding@home simulations of nsp3 macrodomain complex

Open

Maxwell I. Zimmerman;

MD-A001UL

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 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).

Molecular system

Starting structure: 6W02PDB 6W02(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: 3,000
Composition: Molecules of interest
NSP3Protein · 1 chain2,541 atoms167 residues
Total2,541 atoms167 residues
Box dimensions: Dodecahedron

Sequences

Sequence 1Protein · 167 residues

VNSFSGYLKL TDNVYIKNAD IVEEAKKVKP TVVVNAANVY LKHGGGVAGA LNKATNNAMQ VESDDYIATN GPLKVGGSCV LSGHNLAKHC LHVVGPNVNK GEDIQLLKSA YENFNQHEVL LAPLLSAGIF GADPIHSLRV CVDTVRTNVY LAVFDKNLYD KLVSSFL

Run	Outputs
replica 1	Trajectory Analyses

Files

48 files · 119 MB

All files119 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 nsp3 macrodomain complex

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements