Ran both BindCraft and RFdiffusion rather than committing to one.
- Reference/BindCraft 2024: one-button (AF2-multimer-backprop hallucination plus SolubleMPNN refinement in a single tool), tends toward a higher experimental hit rate on well-behaved targets. Good fit for a well-defined round-1 campaign.
- Reference/RFdiffusion 2023 + Reference/ProteinMPNN 2022: more sample count, more control over hotspots and binder length, and the two stages (backbone, then sequence) can be tuned independently. Better for scanning broadly across binding modes, which is why it's the primary line for this round.
Both trace back to the same structure-only design principle Reference/Cao 2022 — RFdiffusion and BindCraft differ in how they generate and score backbones, not in the underlying idea of designing directly against a fixed target structure.
Neither engine is installed on this system yet. For now, results run elsewhere are brought in as imports — see PD-L1/Campaign/PDL1-R1/Run/RF-001.