rfdiffusion

Motif scaffolding with hotspot specification works by defining specific contigmap specifications and hotspot definitions that guide the diffusion model to generate backbones incorporating the desired structural motif. This ensures the generated structures maintain the functional constraints of the target interface.

Yes, symmetric oligomers can be designed using diffusion-based protein generation by applying optional symmetry constraints during the backbone generation process. This allows the model to produce oligomeric structures that maintain the specified symmetry relationships across the generated chains.

To start protein backbone generation, you need a target design objective, compatible checkpoints, and contigmap specifications defining the structural constraints. Optional inputs include hotspot definitions for interface guidance and symmetry constraints for oligomeric designs.

RFdiffusion provides a smooth handoff to downstream steps like ProteinMPNN for sequence design and structure prediction. The generated backbone structures serve as direct input for these downstream tools to validate and assign amino acid sequences.