SMART: An Integrated Platform Revolutionizing Cryo-Electron Microscopy Workflow from Data Acquisition to Atomic Modeling

Recent advancements in cryo-electron microscopy (cryo-EM) have revolutionized structural biology, yet persistent workflow fragmentation between data acquisition, reconstruction, and modeling limits its full potential. This paper presents SMART, the first fully integrated cryo-EM platform unifying three critical AI-driven modules: DataSmart (automated data collection), CryoSmart (3D reconstruction), and ModelSmart (end-to-end atomic modeling). The platform embeds more than 10 distinct AI algorithms across its workflow, achieving unprecedented automation levels. These advancements not only lower the expertise barrier for cryo-EM adoption but also establish a new paradigm for AI-empowered structural biology, with broad implications for high-throughput drug discovery. This protocol provides a comprehensive delineation of the operational procedures for the SMART platform. As an example, this protocol enabled the determination of the 2.1 Å resolution structure of TRPML1, a Ca2 ⁺ -permeable, nonselective, six-transmembrane tetrameric cation channel found in late endosomes and lysosomes (LELs) of mammalian cells. This integrated workflow enables users, including those with minimal cryo-EM experience, to efficiently complete the entire pipeline from data collection to atomic model building.