RFdiffusion3: Institute for Protein Design releases its all-atom protein design model as open-source software, with training code and weights

The University of Washington Institute for Protein Design (Baker lab) released RFdiffusion3 on 3 December 2025: an open-source diffusion model that designs proteins interacting with DNA, small molecules and other molecules at the level of individual atoms, about ten times faster than RFdiffusion2. Training code and model weights are on GitHub through the Rosetta Commons Foundry (pip install rc-foundry[rfd3]). The follow-up paper, "Atomic functional site scaffolding in biopolymers with RFdiffusion3" (Science, doi 10.1126/science.aeh2982, online 15 October 2026 per Crossref), is cited in the Foundry README. Added as an older release Community lacked; speed and benchmark claims are the IPD's own.