article epub_ahead yes Sai A Maddipatla author e957f5e5-91c9-11f0-a95f-e090f66ecb4d Nadav E Sellam author ef280fe0-91c9-11f0-a95f-8dea3f5bc513 Meital I Bojan author 11d88cf5-91ca-11f0-a95f-edf9f08f47b7 Vova Masalitin author ff7958eb-91c9-11f0-a95f-f3bf65828cf6 Sanketh Vedula author Paul Schanda author 7B541462-FAF6-11E9-A490-E8DFE56974250000-0002-9350-7606 Ailie Marx author Alexander Bronstein author 58f3726e-7cba-11ef-ad8b-e6e8cb3904e60000-0001-9699-8730 PaSc department AlBr department GradSch department AlphaFold3 predicts highly accurate protein structures from sequence but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work, we show that AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM) experiments and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology generates compact structural ensembles whose ensemble-averaged observables agree with experiment, with fewer distance restraint violations than traditionally resolved NMR structures and with unmodeled alternate conformations uncovered in electron density. This methodology paves the way for experimentally aware predictive models that generate structural ensembles consistent with the measurements, potentially over multiple modalities, and that can be further refined toward thermodynamically grounded ensembles by incorporating energetics. Springer Nature2026 eng 1087-0156 1546-1696 4237411410.1038/s41587-026-03166-5 Maddipatla, Sai A., et al. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” <i>Nature Biotechnology</i>, Springer Nature, 2026, doi:<a href="https://doi.org/10.1038/s41587-026-03166-5">10.1038/s41587-026-03166-5</a>. S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, Nature Biotechnology (2026). Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Masalitin, V., Vedula, S., Schanda, P., … Bronstein, A. M. (2026). Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. <i>Nature Biotechnology</i>. Springer Nature. <a href="https://doi.org/10.1038/s41587-026-03166-5">https://doi.org/10.1038/s41587-026-03166-5</a> Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Vova Masalitin, Sanketh Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” <i>Nature Biotechnology</i>. Springer Nature, 2026. <a href="https://doi.org/10.1038/s41587-026-03166-5">https://doi.org/10.1038/s41587-026-03166-5</a>. Maddipatla SA, Sellam NE, Bojan MI, Masalitin V, Vedula S, Schanda P, Marx A, Bronstein AM. 2026. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. S. A. Maddipatla <i>et al.</i>, “Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles,” <i>Nature Biotechnology</i>. Springer Nature, 2026. Maddipatla SA, Sellam NE, Bojan MI, et al. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. <i>Nature Biotechnology</i>. 2026. doi:<a href="https://doi.org/10.1038/s41587-026-03166-5">10.1038/s41587-026-03166-5</a> 222682026-07-12T22:02:19Z2026-07-13T09:34:36Z