Protein complex prediction with AlphaFold-Multimer

Abstract

While the vast majority of well-structured single protein chains can now be predicted to high accuracy due to the recent AlphaFold [1] 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 benchmark dataset of 17 heterodimer proteins without templates (introduced in [2]) we achieve at least medium accuracy (DockQ [3] ≥ 0.49) on 14 targets and high accuracy (DockQ ≥ 0.8) on 6 targets, compared to 9 targets of at least medium accuracy and 4 of high accuracy for the previous state of the art system (an AlphaFold-based system from [2]). We also predict structures for a large dataset of 4,433 recent protein complexes, from which we score all non-redundant interfaces with low template identity. For heteromeric interfaces we successfully predict the interface (DockQ ≥ 0.23) in 67% of cases, and produce high accuracy predictions (DockQ ≥ 0.8) in 23% of cases, an improvement of +25 and +11 percentage points over the flexible linker modification of AlphaFold [4] respectively. For homomeric interfaces we successfully predict the interface in 69% of cases, and produce high accuracy predictions in 34% of cases, an improvement of +5 percentage points in both instances.