Inference-time projection for physically valid AlphaFold 3–style biomolecular diffusion models (arXiv:2610.07037v1)
The paper proposes treating physical validity as a constrained inference problem and introduces two closed-form projection operators—an inter-chain van der Waals projection and a ligand distance-geometry projection—applied to the diffusion model's denoised coordinate estimate (x̂0). The operators are local, sparse, displacement-capped, require no network evaluations or gradients, and — when applied to Boltz-2 and OpenFold-3 across five benchmarks (CASP15, CASP16, PoseBusters monomer and complex sets, and the Boltz physical-validity set) — recover perfect physical validity while preserving structural-accuracy and ligand-placement metrics with negligible runtime and memory overhead.