foundry Scaffolded diffusion in rfd3

Hi there.

Happy to see the new version. I was mostly working with the original rfdiffusion and really enjoyed the feature to provide a target pdb to guide diffusion towards a specific structure, and at the same time provide hotspots for binder design (I think in the original version it was called "ppi-scaffolded"). From the documentation I was not immediately able to deduct whether this feature still exists in rfd3.

Any insights on this?

Thanks so much

Best

Toby

Dec 09 '25 02:12 Cookiemaster33

A great issue! I meet the same trouble. Please tell me if scaffold is available in rdf3.

Dec 09 '25 03:12 hmLin2002

Hi! There's select_hotspots which you can specify. The other two guidance options are select_buried / select_exposed and COM guidance with ori_token.

Dec 13 '25 07:12 Ubiquinone-dot

Ok. Gotcha.

What is COM? I tried to find it on the GitHub, but wasn't able to find a description.

Best

Toby

Dec 14 '25 16:12 Cookiemaster33

COM stands for center of mass. The ORI token specifies where the center of mass of your designed structure should be.

Dec 15 '25 18:12 rclune