FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila

Protein-protein interactions (PPIs) are fundamental to cellular function. Yet most Drosophila PPIs remain structurally uncharacterized despite the wealth of genetic and biochemical data available for this organism. Here we present FlyPredictome, a structural interactome based on 1.5 million pairwise AlphaFold-Multimer predictions. Using a local confidence metric that performs robustly for interactions involving flexible and disordered proteins, we systematically assess experimentally reported Drosophila PPIs and predict direct binding interfaces at residue-level resolution. Testing their functional relevance, we find that phenotype-associated missense mutations are enriched at predicted interaction interfaces. Building on these validated predictions, we construct an evidence-supported PPI network, revealing modular organization from signaling pathways to individual protein complexes. FlyPredictome is available as an open database, providing a structural foundation for interaction discovery in Drosophila.