Folding@home simulations of nsp13

Markov state model built from 3.4 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).

Molecular system

Starting structure: 6JYTPDB 6JYT(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
NSP13Protein · 1 chain9,291 atoms596 residues
Total9,291 atoms596 residues
Box dimensions: Dodecahedron

Sequences

Sequence 1Protein · 596 residues

AVGAXVLXNS QTSLRXGAXI RRPFLXCKXC YDHVISTSHK LVLSVNPYVX NAPGXDVTDV TQLYLGGMSY YXKSHKPPIS FPLCANGQVF GLYKNTCVGS DNVTDFNAIA TCDWTNAGDY ILANTCTERL KLFAAETLKA TEETFKLSYG IATVREVLSD RELHLSWEVG KPRPPLNRNY VFTGYRVTKN SKVQIGEYTF EKGDYGDAVV YRGTTTYKLN VGDYFVLTSH TVMPLSAPTL VPQEHYVRIT GLYPTLNISD EFSSNVANYQ KVGMQKYSTL QGPPGTGKSH FAIGLALYYP SARIVYTACS HAAVDALCEK ALKYLPIDKC SRIIPARARV ECFDKFKVNS TLEQYVFCTV NALPETTADI VVFDEISMAT NYDLSVVNAR LRAKHYVYIG DPAQLPAPRT LLTKGTLEPE YFNSVCRLMK TIGPDMFLGT CRRCPAEIVD TVSALVYDNK LKAHKDKSAQ CFKMFYKGVI THDVSSAINR PQIGVVREFL TRNPAWRKAV FISPYNSQNA VASKILGLPT QTVDSSQGSE YDYVIFTQTT ETAHSCNVNR FNVAITRAKV GILCIMSDRD LYDKLQFTSL EIPRRN

Run	Outputs
replica 1	Trajectory Analyses

Files

50 files · 1.4 GB

All files1.4 GB

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 nsp13

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements