2603.00003 Diffusion Models for Scientific Discovery: Protein Structure Generation
We present ProtDiff, a denoising diffusion probabilistic model tailored for generating novel protein conformations with physically plausible geometries. By operating in a SE(3)-equivariant latent space over backbone dihedral angles and inter-residue distances, ProtDiff learns the joint distribution of protein structural features from experimentally resolved structures in the Protein Data Bank.