Path C - Module 34: Comparison & Superposition

When you compare two different potential drugs, you need to align their binding poses. In this module, you will learn to superimpose different Mpro complexes to see how their inhibitors match.

import molsysmt as msm

# Align 6LU7 (Crystal) and another pose
molsys1 = msm.convert('pdb:6LU7', to_form='molsysmt.MolSys')
molsys2 = msm.copy(molsys1)

# Measure similarity
rmsd = msm.structure.least_rmsd_align(molsys2, reference_molecular_system=molsys1)
print(f"Pose similarity (RMSD): {rmsd}")

WARNING: Cross-chain covalent bonds were detected. (Hint: Verify whether these bonds are expected in your system. Docs: https://www.uibcdf.org/MolSysMT)

Pose similarity (RMSD): <molsysmt.native.molsys.MolSys object at 0x7f08ec98fd90>