BioEmu (Microsoft)

BioEmu from Microsoft Research is a generative diffusion model that emulates the equilibrium ensemble of shapes a protein moves between, trained on molecular dynamics simulations and experimental data. Rather than predicting one static structure, the Science 2025 paper shows it sampling conformational ensembles and estimating folding free energies thousands of times faster than simulation. For cancer drug discovery this matters for cryptic pockets, binding sites that only open transiently, as in KRAS, which static structure predictors cannot reveal. Its predictions are approximate, and the published work focuses on small proteins, so large complexes and membrane proteins remain beyond validated use. For a newcomer: BioEmu predicts how a protein wiggles, which can reveal hidden pockets a drug might fit into.