Folding@home simulations of nsp3 pl2pro domain

Open

Maxwell I. Zimmerman;

MD-A001UM

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 731 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: 3E9SPDB 3E9S(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 chain4,927 atoms314 residues
Total4,927 atoms314 residues
Box dimensions: Dodecahedron

Sequences

1

Sequence 1Protein · 314 residues

EVRTIKVFTT VDNINLHTQV VDMSMTYGQQ FGPTYLDGAD VTKIKPHNSH EGKTFYVLPN DDTLRVEAFE YYHTTDPSFL GRYMSALNHT KKWKYPQVNG LTSIKWADNN CYLATALLTL QQIELKFNPP ALQDAYYRAR AGEAANFCAL ILAYCNKTVG ELGDVRETMS YLFQHANLDS CKRVLNVVXK TXGQQQTTLK GVEAVMYMGT LSYEQFKKGV QIPXTXGKQA TKYLVQQESP FVMMSAPPAQ YELKHGTFTC ASEYTGNYQC GHYKHITSKE TLYCIDGALL TKSSEYKGPI TDVFYKENSY TTTI

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

49 files · 230 MB

All files230 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.