Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3 (opens in new tab)

Accurate prediction of protein complex structures by AlphaFold3 and similar programs has been used to predict the presence of protein–protein interactions (PPIs), but this technique has never been applied to an entire genome due to onerous computational requirements and questionable utility. Here we present pooled-PPI prediction, a technique that dramatically improves the accuracy of genome-scale screens compared to a paired approach while simultaneously reducing inference time (~twofold) and...