Summary
Low-pLDDT hallucinations from AlphaFold3-generation methods are designable (1). Out of the various methods tested, Boltz showed the best designability, with poly-”X” sequences adopting designable backbones. Design benefit from multiple iterations.
See also
References
1.
Cho Y, Rangel G, Bhardwaj G, Ovchinnikov S. Protein Hunter: exploiting structure hallucination within diffusion for protein design. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.10.10.681530