Overview

This repository contains 62 PROTAC structures predicted with AlphaFold 3 and Boltz-1, and 2 molecular dynamics trajectories, reported in the publication:  

"Predicting PROTAC-Mediated Ternary Complexes with AlphaFold3 and Boltz-1"  
by Nils Dunlop, Francisco Erazo, Farzaneh Jalalypour, Rocío Mercado

The accompanying code is available at: https://github.com/NilsDunlop/PROTACFold/.  

AlphaFold 3 Output Terms of Use

By using this information, you agree to the AlphaFold 3 Output Terms of Use, found at:  
https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md.  

To request access to the AlphaFold 3 model parameters, follow the process outlined at:  
https://github.com/google-deepmind/alphafold3.  

You may only use these parameters if received directly from Google. Use is subject to terms of use available at:  
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.  

All-Atom Molecular Simulations

In addition to the AlphaFold 3-predicted structures, this repository includes all-atom molecular simulations of the PROTAC ternary complex (PDB ID: 9B9W, AF3-predicted complex) using GROMACS with the Amber force field. 

Simulation Details  

• Two independent 300 ns replicas (Rep1 and Rep2)  
• Trajectory data saved at 5 ns intervals  

File Descriptions  

Replica 1 (Rep1) - 300 ns Simulation  

• structure.gro → Structure file containing the entire system 
• structure_complex.gro → Structure file containing the complex (excluding water and ions)  
• Structure.tpr → Portable binary run input file  
• Rep1.xtc → Trajectory file (excluding water and ions)  
• Rep1.mov → QuickTime movie of the simulation  

Replica 2 (Rep2) - 300 ns Simulation

• structure.gro → Structure file containing the entire system  
• structure_complex.gro → Structure file containing the complex (excluding water and ions)  
• Structure.tpr → Portable binary run input file  
• Rep2.xtc → Trajectory file (excluding water and ions)  
• Rep2.mov → QuickTime movie of the simulation  

Contact Information  

For any inquiries regarding this dataset, please contact: rocio.mercado@chalmers.se.