rfd3-reference

RFdiffusion3 uses contig syntax to define chain lengths and breaks, such as "60-80,/0,60-80" for a two-chain protein design. This syntax maps directly to the generated structural topology.

RFdiffusion3 supports various symmetry types for designing symmetric oligomers. Best practices include using optimal batch sizes for symmetry generation to ensure successful computational protein design outputs.

Use the `select_fixed_atoms` and `select_hotspots` input parameters in RFdiffusion3 to constrain specific structural regions during protein binder design. These parameters anchor the design to desired interaction interfaces.

The RFdiffusion3 Foundry API has known limitations compared to the RFdiffusion v1/v2 CLI features. Users should review these constraints to ensure their specific protein design scenarios are fully supported.

Best practices for small molecule binders and enzymes involve specific RFdiffusion3 conditioning parameters and understanding expected success rates. Proper parameter tuning is essential for functional computational protein design.

You should avoid RFdiffusion3 if your design requires unsupported CLI features absent from the Foundry API, or if your scenario exceeds the expected success rates for specific conditioning without extensive downstream validation.