Summary
Protein backbone design methods can be repurposed for modeling dynamics into electron density derived from either crystallography or cryo-EM (1). Here the method Chroma was used, and fit to electron density was captured as a score that could supplement the score used by the diffusion model. The same kind of guidance does not require experimental density: shape potentials can steer backbone diffusion toward arbitrary user-specified global protein shapes (2).
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Ref (1)
1.
Maddipatla SA, Sellam NB, Vedula S, Marx A, Bronstein A. Generative modeling of protein ensembles guided by crystallographic electron densities. 2024; Available from: https://arxiv.org/abs/2412.13223
2.
Qi Y, Zhang G, Yserentant K, Lee S, Lyubimov A, Ibrahim K, et al. Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion. 2026. Available from: https://doi.org/10.64898/2026.07.22.740177