Path A - Module 30: Geometrical Measurements#

Now that you have built your therapeutic complex, you need to prove that it actually “fits”. Geometry is the first indicator of affinity.

In this module, you will learn to measure the spatial relationships between your peptide and the Alzheimer’s fibril.

import molsysmt as msm
from molsysmt import systems

# Load a pre-built complex (fibril + peptide)
fibril = msm.convert('pdb:2BEG', to_form='molsysmt.MolSys')
peptide = msm.build.build_peptide('KLVFF')
molsys = msm.merge([fibril, peptide])

1. Simple Distances#

Let’s measure the distance between the center of the peptide and the center of the fibril core.

dist = msm.get_distances(molsys, selection='molecule_type=="peptide"', 
                         selection_2='chain_index==2', center_of_selection=True)

print(f"Distance between centers: {dist}")

2. Finding the Closest Contact#

Usually, we want to know the minimum distance between any atom of the peptide and any atom of the target. This tells us if they are effectively touching.

min_dist = msm.get_minimum_distances(molsys, selection='molecule_type=="peptide"', 
                                     selection_2='molecule_type=="protein"')

print(f"Minimum contact distance: {min_dist}")

3. Measuring Orientation (Angles)#

Orientation is as important as distance. Let’s measure the angle between three specific C-alpha atoms that define the interface.

# Pick 3 atom indices (just examples for the tutorial)
atom_indices = [10, 500, 1400]

angle = msm.get_angles(molsys, selection=atom_indices)
print(f"Angle between atoms {atom_indices}: {angle}")

🏆 Path A Challenge: The Geometric Analyst#

  1. Calculate the distance matrix between all residues of the peptide and all residues of the first chain of the fibril.

  2. Find which residue of the peptide is closest to the fibril.

  3. Use msm.structure.get_dihedral_angles() to check the conformation of that specific residue.

Geometry is the foundation of structural biology. In Module 31, we will move from numbers to regions and explore the Proximity and Neighborhoods around our peptide.