While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes
remains a challenge in many cases. In this work, we demonstrate that an AlphaFold model
trained specifically for multimeric inputs of known stoichiometry, which we call AlphaFold-
Multimer, significantly increases accuracy of predicted multimeric interfaces over input-
adapted single-chain AlphaFold while maintaining high intra-chain accuracy. On a …