Folding@home simulations of nsp5 dimer

Open

Maxwell I. Zimmerman;

MD-A001UN

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)

Description

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).

Molecular system

Starting structure: 6Y2EPDB 6Y2E(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: 5,000
Composition: Molecules of interest
NSP5Protein · 1 chain9,364 atoms612 residues
Total9,364 atoms612 residues
Box dimensions: Dodecahedron

Sequences

1

Sequence 1Protein · 306 residues

SGFRKMAFPS GKVEGCMVQV TCGTTTLNGL WLDDVVYCPR HVICTSEDML NPNYEDLLIR KSNHNFLVQA GNVQLRVIGH SMQNCVLKLK VDTANPKTPK YKFVRIQPGQ TFSVLACYNG SPSGVYQCAM RPNFTIKGSF LNGSCGSVGF NIDYDCVSFC YMHHMELPTG VHAGTDLEGN FYGPFVDRQT AQAAGTDTTI TVNVLAWLYA AVINGDRWFL NRFTTTLNDF NLVAMKYNYE PLTQDHVDIL GPLSAQTGIA VLDMCASLKE LLQNGMNGRT ILGSALLEDE FTPFDVVRQC SGVTFQ

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

55 files · 719 MB

All files719 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

Contributors

Research groups: University of Pennsylvania, Bowman lab

Acknowledgements

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