SARS-CoV-2 papain-like protease (PLpro): inhibitor accessibility is promoted by the BL2-loop region.
Molecular dynamics analysis of PLpro conformational dynamics, combining PCA, Markov state models, inter-domain angles and dihedral analysis.
| File | Description |
|---|---|
PCA-PLPpro-gmf.ipynb, PCA-PLPpro.sh |
Principal component analysis of the PLpro trajectories and the script used to run it |
MSM_PLPpro.ipynb |
Markov state model (PyEMMA): featurization, clustering, implied timescales, metastable states |
Angle-between-domain.ipynb |
Angle between protein domains along the trajectory (MDAnalysis) |
Dihedral-plpro.ipynb |
Dihedral angle distributions |
n5states_state01–05.pdb |
Representative structures of the five metastable states |
PLPprofreeE.eps, PLPprometas.eps |
Free-energy landscape and metastable-state figures |
Python 3 with Jupyter and the libraries listed below. Trajectories and Schrödinger Suite outputs are not included in this repository.
pip install jupyter numpy pandas matplotlib seaborn MDAnalysis pyemma mdtraj nglview mdshareGlaucio Monteiro Ferreira — Research Associate, Institute of Chemistry, University of São Paulo (IQ-USP) · LIBNM · Ferreira Lab · ORCID · FAPESP profile · gmf@usp.br