Two inference-time fixes make biomolecular predictions physically valid
A new inference-time method makes AF3-style biomolecular cofolding outputs physically valid without retraining, helping researchers use predicted complexes without changing the model. It projects the denoiser's coordinates to separate clashing chains and repair ligand geometry, including bond lengths, planarity, and chirality, using no extra network evaluations or gradients. On Boltz-2 and OpenFold-3 across five benchmarks, it recovered perfect physical validity while preserving structural-accuracy and ligand-placement metrics with negligible runtime and memory overhead.