Summary
Increasing the number of diffusion samples from all-atom protein structure prediction methods is sufficient to increase the fraction of correctly docked poses (1). This is in contrast with conformational sampling, where several cases have been shown of biomolecular diffusion models being unable to reproduce equilibrium dynamics of biological systems.
Figures
Ref (1)
1.
Smorodina E, Ali M, Kropivšek Brumat K, Salicari L, Miklavc S, Kappassov A, et al. Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.03.02.709004