OLIGAMIX

OLIGAMIX is a lightweight and extensible analysis tool for tracking oligomerization states and inter-chain contact networks from molecular dynamics (MD) simulations.

The name OLIGAMIX is a portmanteau of “oligomerization” and “dynamics”, reflecting its core goal of capturing the dynamic assembly and evolution of multimeric protein systems. Designed to capture the dynamic assembly of multimeric protein systems, OLIGAMIX computes time-resolved oligomerization sizes and generates residue–residue contact maps that quantify interface formation across trajectories. It is particularly suited for studying protein aggregation, self-assembly, and interface stability in systems such as amyloids, membrane complexes, or intrinsically disordered regions. The framework supports trajectory files in standard formats (.xtc, .dcd, .trr, etc.), uses user-defined cutoffs for defining contacts and clusters, and outputs both raw data and publication-ready plots.

🧪 OLIGAMIX was originally developed to support the comparative analysis of force-field-dependent aggregation pathways presented in the study:
“Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations”
J. Chem. Inf. Model., 2020, DOI: 10.1021/acs.jcim.0c01063

Following dependencies need to be fulfilled to run the codes.

• Python 2.7 or 3.6 (From Anaconda distribution)
• MDanalysis (conda install -c conda-forge mdanalysis)
• MDtraj (conda install -c omnia mdtraj)

Calculation of intermolecular residue-residue contact map and oligomer state among the protein chains

The oligos-cmap.py code calculates the highest oligomer state formed by protein chains in the system within a specfic cutoff distance. It indicates the time (in the form of snaphots from simulation trajectory) at which dissociation or association of protein chains occurs and also identifies the protein chains involved in aggregated state.
Copy/Download the codes to the analysis directory consisting of the reference PDB structure (.pdb file, other formats can be tested), the molecular dynamics trajectory file only with protein atoms (.xtc file, other formats can be tested) and the Minimum distance in nano-metres(nm) to consider association or aggregation of proteins.

Usage: python2 oligos-cmap.py <.pdb file> <.xtc file> <distance in Angstrom>

Output files:
- oligomer-groups.dat - groups the interacting protein chains.
- oligomer-states.dat - counts the number of chains in each oligomer group.
- oligo-highest-size.dat - finds the maximum oligomer size formed per frame. (maximum size = total number of protein chains in simulation box)
- contact-map.dat - saves the frequency of contacts between residues from different proteins.
- oligo-block-average.dat - creates a series of 25-frame moving average of the maximum oligomer size.

Plotting the Inter-residue Contact Map:

Usage: python3 plot-cmap.py <.pdb file> <.xtc file> contact-map.dat

Output files: Contact-map.pdf - Image file indicating average frequency of contacts between residues

Plotting the Oligomerisation state:

Usage: python3 plot-oligostate.py <.pdb file> <.xtc file> oligo-highest-size.dat <simulation time in nanoseconds(ns)>

Output files: Oligomerisation-state.pdf - Image file indicating evolution of aggregation kinetics over time

Note: <filename>.dat files are output files.

----------------------------------------------------- Usage examples -----------------------------------------------------
Walkthrough the codes using the sample structure and trajectory files in example.zip
Usage:

• python2 oligos-cmap.py protein_ref.pdb protein_md.xtc 4
• python3 plot-cmap.py protein_ref.pdb protein_md.xtc contact-map.dat
• python3 plot-oligostate.py protein_ref.pdb protein_md.xtc oligo-highest-size.dat 1000