Predicting PROTAC-Mediated Ternary Complexes with AlphaFold3 and Boltz-1

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. Boltz-1 Output Terms of Use Boltz-1 predictions in this dataset are released under the MIT License, making them freely available for both academic and commercial purposes. All code and weights are provided under MIT license. For more information, please refer to the Boltz-1 repository at: https://github.com/jwohlwend/boltz 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: [e-mail].