Summary
Protein structural ensembles can be sampled with AlphaFold3 and related methods to match experimental data like X-ray or EM density, or NMR NOEs, by using guidance sampling (1). AF3 by default predicts tighter conformational ensembles.
1.
Maddipatla SA, Bojan N, Bojan M, Vedula S, Schanda P, Marx A, et al. Inverse problems with experiment-guided AlphaFold. In: International Conference on Machine Learning. PMLR; 2025. p. 42366–93. Available from: https://proceedings.mlr.press/v267/maddipatla25a.html