PT  - JOURNAL ARTICLE
AU  - P. Bryant
AU  - G. Pozzati
AU  - A. Elofsson
TI  - Improved prediction of protein-protein interactions using AlphaFold2
AID  - 10.1101/2021.09.15.460468
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.09.15.460468
4099  - http://biorxiv.org/content/early/2021/12/15/2021.09.15.460468.short
4100  - http://biorxiv.org/content/early/2021/12/15/2021.09.15.460468.full
AB  - Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimized multiple sequence alignments, generate models with acceptable quality (DockQ≥0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR. The protocol can be found at: https://gitlab.com/ElofssonLab/FoldDock.Competing Interest StatementThe authors have declared no competing interest.