Nsp16 monomer from SARS-CoV-2

Open

Neha Vithani;Michael D Ward;Maxwell I. Zimmerman;Gregory R. Bowman;

MD-A001U9

Created: 9 Jun 2022
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 770 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).

Molecular system

Starting structure: 6W4HPDB 6W4H(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: 5,001
Composition: Molecules of interest
NSP16Protein · 1 chain4,673 atoms298 residues
Total4,673 atoms298 residues
Box dimensions: Dodecahedron

Sequences

Sequence 1Protein · 298 residues

SSQAWQPGVA MPNLYKMQRM LLEKCDLQNY GDSATLPKGI MMNVAKYTQL CQYLNTLTLA VPYNMRVIHF GAGSDKGVAP GTAVLRQWLP TGTLLVDSDL NDFVSDADST LIGDCATVHT ANKWDLIISD MYDPKTKNVT KENDSKEGFF TYICGFIQQK LALGGSVAIK ITEHSWNADL YKLMGHFAWW TAFVTNVNAS SSEAFLIGCN YLGKPREQID GYVMHANYIF WRNTNPIQLS SYSLFDMSKF PLKLRGTAVM SLKEGQINDM ILSLLSKGRL IIRENNRVVI SSDVLVNN

Run	Outputs
replica 1	Trajectory Analyses

Files

50 files · 385 MB

All files385 MB

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Acknowledgements

We are grateful to the citizen scientists who contribute to Folding@home by running simulations on their personal computers. This work was funded by NSF CAREER Award MCB-1552471, NSF RAPID 58628, NIH R01 GM124007 and RF1AG067194