This project is to show how we can run the molecular docking for the PFAS into protein systems, including the conventional AutoDock Vina and AlphaFold 3.
It has several useful files that can help us to go through this project.
- "tutorials" folder
It includes the tutorials on how to use the computational tools to study the protein-PFAS interactions step-by-step.
- "scripts" folder
It includes the necessary python and bash scripts to run the docking jobs.
- "data" folder
It includes some essential data files used to show the results quickly.
You can directly "git clone" this resporsitory, and these scripts can be directly executed by python and bash.
git clone https://github.com/XipingGong/pfas_docking.git
However, you need to change some parameters and install other essential packages, like the MDTraj, etc.
Gong, X. et al. Assessing AlphaFold 3 for Per- and Polyfluoroalkyl Substances (PFAS) Docking in Protein Structures, 2025 (Submitted)
Gong, X. et al. AF3-Vina-MMPBSA Method for PFAS Docking in Proteins (Preparation)