Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta

Cryogenic electron microscopy (cryo-EM) has become a widely used technique for determining the three-dimensional structures of biological macromolecules. Despite its advantages, building accurate structural models from cryo-EM data remains challenging, particularly at non-atomic resolutions. Here, we present CryoZeta, a de novo structure modeling program that leverages a diffusion-based generative deep neural network to integrate cryo-EM map density features with a biomolecular structure prediction pipeline similar to Alphafold3. By jointly leveraging sequence information and density-based features, CryoZeta generates highly accurate structural models that are consistent with the experimental map density. Evaluated on benchmark datasets covering protein complexes, protein-nucleic acid assemblies, and nucleic acid-only systems at resolutions up to 10 Å, CryoZeta consistently outperforms existing cryo-EM modeling methods in atomic accuracy. These results highlight the benefits of directly incorporating cryo-EM density into modern structure prediction pipelines and establish the method as a robust tool for automated, high-fidelity modeling from cryo-EM maps.