Mast Cell Activation and Polymer Immunogenicity – Supplementary Materials

Mast Cell Activation and Polymer Immunogenicity – Supplementary Materials 
This repository contains all data and scripts used in the study
“Molecular Basis of Polyethylene Glycol Immunogenicity and the Biocompatibility of Polyglycerol”
by Alexandro da Silva Nunes. 
Contents 
model/ – SBML version of the extended mast cell model (including Autotaxin and LPA feedback).
data/ – Time‐course simulation results (CSV) of all species (histamine, IL‐6, LPC, LPA, autotaxin, etc.).
figures/ – Publication‐ready PNG figures: 
main/ – Main figures (Fig. 1–10 as in the manuscript).
supplementary/ – Supplementary figures (S1–S12).
scripts/ – Python scripts to reproduce all simulations and figures: 
run_and_plot.py – Runs the Tellurium simulation and generates time‐course plots.
final_phase_v.py – Minimal script for simulation and SBML export.
plot_mmpbsa_fig5.py – Generates MMPBSA binding energy figure.
plot_sensitivity_fig8.py – Generates Morris sensitivity figure.
analyse_ige.py – Processes IgE MD trajectories and generates PCA/RMSF plots.
analyse_lnp.py – Processes LNP MD trajectories and generates energy/distance plots.
gerar_todas_figuras.py – Master script to regenerate all figures.
mmpbsa/ – Input files and scripts for MMPBSA calculations (PEG‐IgE and PGL‐IgE). 
Requirements 
Python 3.9+ with Tellurium, pandas, numpy, matplotlib, SALib, scipy.
GROMACS 2022.3 (for MD simulations) and the Martini 3 force field (provided in scripts/).
For MMPBSA: gmx_MMPBSA (install via pip install gmx_MMPBSA). 
Reproducing the Workflow 
Tellurium simulations
cd scripts && python run_and_plot.py
This will generate simulation_results.csv and all time‐course figures.
MMPBSA figures
python plot_mmpbsa_fig5.py (requires gmx_MMPBSA and the trajectories in mmpbsa/).
Sensitivity analysis
python plot_sensitivity_fig8.py (requires SALib).
MD analysis (if you have the raw trajectories) 
For IgE: python analyse_ige.py --pdb 2wqr.pdb --traj 2wqr.xtc
For LNPs: python analyse_lnp.py --top peg_lnp.tpr --traj peg_lnp.xtc
Regenerate all figures
python gerar_todas_figuras.py 
License 
This work is licensed under the MIT License.