Path C - Module 35: Principal Components (PCA) & Axes

Does the binding of your drug restrict the motion of the protease? To understand how an inhibitor works, you need to see how it affects the essential dynamics of the enzyme.

In this module, you will learn to use PCA to identify the breathing motions of the SARS-CoV-2 Mpro.

import molsysmt as msm
from molsysmt import systems

# Load Mpro trajectory proxy
villin_traj = systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.dcd']
villin_topo = systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm']
molsys = [villin_topo, villin_traj]

# Perform PCA
eigenvectors, eigenvalues = msm.structure.principal_component_analysis(molsys, selection='atom_name=="CA"')
# The first dimensionless eigenvector is PC1; its eigenvalue has units of nm**2.
print(f"Main mode of motion variance: {eigenvalues[0]:.2f}")

WARNING: Structural attributes were dropped because only an item outside the structure axis of the molecular system provides them: atom_index, structure_chemical_state_index, structure_id, time. (Hint: A file holding a single reference conformation cannot supply a series for a whole trajectory. Take the attribute from the trajectory item, or convert first. Docs: https://www.uibcdf.org/MolSysMT)

Main mode of motion variance: 101.59 nanometer ** 2