Summary
Predicted changes in binding affinity of PPIs by AlphaFold3 are orthogonal to those made by other methods, and can be ensembled with favorable results (1). AF3 outperforms other deep learning-based methods such as Inverse folding methods and Protein language models. Its predictions can be improved by ensembling with those from force fields, but not other deep learning methods. It is unclear if those predictions are better than those from force fields alone.
Figures
Figure 2 from (1)
1.
Lu W, Zhang J, Rao J, Zhang Z, Zheng S. AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions. openRxiv; 2024. Available from: https://doi.org/10.1101/2024.05.25.595871