AdsPro computes the adsorbed conformation and free energy of adsorption (ΔG_ads) of a protein on a nanoparticle surface using coarse-grained molecular dynamics and Potential of Mean Force (PMF) calculations.
It is the single-protein adsorption engine powering SurfCo — the protein corona composition simulator. For each protein-NP pair, AdsPro answers: In what orientation does this protein adsorb, and how strongly?
https://danaresearchgroup.github.io/AdsPro/
The documentation covers:
- Installation
- Quick Start
- Configuration Reference
- Methods — Physics & Mathematics
- Extending to New Surfaces
- Output & Validation
git clone https://github.com/DanaResearchGroup/AdsPro.git
cd AdsPro
chmod +x install.sh && ./install.sh
source ~/adspro-venv/bin/activate
python -m adspro --project exampleOpen projects/example/Lysozyme/adspro_result.html in your browser to view the result.
Lysozyme on silica NP (R = 71.3 nm, ζ = −50 mV, 20 mM NaCl, pH 7.4):
| Metric | Value |
|---|---|
| ΔG_ads | −28.8 kJ/mol |
| WHAM converged | Yes |
| Contact residues | 31 (ARG/LYS dominant) |
| Native contact retention | 73.5% |
| All-atom MD | AdsPro | |
|---|---|---|
| Time per protein | Weeks–months (HPC) | Hours (workstation) |
| New surface cost | Weeks of force-field work | 1 day chromatography |
| 20-protein corona study | Years | ~2 days |
Developed at the Dana Research Group, Technion — Israel Institute of Technology.
- Benjamin Shugaev (lead developer)
- Dr. Alon Grinberg Dana (principal investigator)