Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3
Creators
Description
Overview
This repository contains 48 structures predicted with AlphaFold 3, and 2 molecular dynamics trajectories, reported in the publication:
"Enhancing PROTAC Ternary Complex Prediction with Ligand Information in AlphaFold 3"
by Francisco Erazo, Nils Dunlop, 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.
Files
5HXB.zip
Files
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Additional details
Software
- Repository URL
- https://github.com/NilsDunlop/PROTACFold/
- Programming language
- Python