Genome-scale prediction of protein structures and their interactions offers significant potential for advancing our understanding of biology. However, its broader application has been constrained by the high computational demands involved. In recent years, advances in protein structure prediction–most notably the introduction of AlphaFold3–have marked major progress in the field. Building on these developments, we have created a tool FlashFold that enables protein structure prediction up to three times faster than AlphaFold3, while maintaining comparable accuracy. Our goal is to apply FlashFold for genome-scale prediction of protein-protein interactions (PPI) to uncover novel interaction partners.