Summary
PDB-derived fragments selected for surface complementarity can guide diffusion toward more structurally diverse binders (1). This could be due to the seeds helping overcome structural sampling biases of diffusion models and making elongated rather than compact proteins.
See also
- No one-size-fits-all best approach to motif scaffolding protein design
- Diffusion-based protein design methods undersample structural diversity in specific topologies
1.
Britton D, Ghose DA, Halpin JC, Birnbaum F, Gundu K, Raval S, et al. Seed-Guided De Novo Design Expands the Structural Diversity of Antitoxin Protein Binders. bioRxiv : the preprint server for biology. 2026; Available from: https://doi.org/10.64898/2026.08.02.742339