Zhu_Sisk_AR_oligomers_2025

Code Accompanying "How small molecules stabilize oligomers of a phase-separating intrinsically disordered protein"

This repository contains scripts and Jupyter notebooks for analyzing the Tau-5_R2 dimer simulations in the apo, EPI-002–bound, and 1aa–bound conditions.

The molecular dynamics trajectories used in this manuscript can be downloaded here:

https://www.dropbox.com/scl/fi/ee6jmg26bgbzz7omb28rm/Zhu_et_al_dimer.zip?rlkey=vunfzpbij6tlpncj8bxqcl0k2&dl=0

Place all downloaded trajectory files in a folder named trajectory/ before running any notebooks.

📖 Reading the Trajectories in Python

Load protein-only trajectories

import mdtraj as md

traj_apo = md.load('trajectory/apo.protein.100us.stride100.dcd',
                   top='trajectory/R2_dimer.pdb')

traj_E2 = md.load('trajectory/E2.protein.100us.stride100.dcd',
                  top='trajectory/R2_dimer.pdb')

traj_1AA = md.load('trajectory/1AA.protein.85us.stride100.dcd',
                   top='trajectory/R2_dimer.pdb')

Load protein+ligand trajectories

import mdtraj as md

traj_E2_lig = md.load('trajectory/E2.protein.ligand.100us.stride100.dcd',
                      top='trajectory/R2_dimer_epi002.pdb')

traj_1AA_lig = md.load('trajectory/1AA.protein.ligand.85us.stride100.dcd',
                       top='trajectory/R2_dimer_1aa.pdb')