Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models

[Display omitted] •Resolving protein structural variability is key to understanding their mechanisms.•Improved machine learning method facilitates high-resolution heterogeneity analysis.•Integration of molecular models improves performance and interpretability. Resolving the structural variability of proteins is often key to understanding the structure–function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with machine learning algorithms, provides a way to reveal the dynamics within the protein system from noisy micrographs. Here, we introduce an improved computational method that uses Gaussian mixture models for protein structure representation and deep neural networks for conformation space embedding. By integrating information from molecular models into the heterogeneity analysis, we can analyze continuous protein conformational changes using structural information at the frequency of 1/3 Å−1, and present the results in a more interpretable form.