DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation

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Abstract

Atomic structure modeling is a crucial step in determining the structures of protein complexes using cryo-electron microscopy (cryo-EM). This work introduces DEMO-EMol, an improved server that integrates deep learning-based map segmentation and chain fitting to accurately assemble protein-nucleic acid (NA) complex structures from cryo-EM density maps. Starting from a density map and independently modeled chain structures, DEMO-EMol first segments protein and NA regions from the density map using deep learning. The overall complex is then assembled by fitting protein and NA chain models into their respective segmented maps, followed by domain-level fitting and optimization for protein chains. The output of DEMO-EMol includes the final assembled complex model along with overall and residue-level quality assessments. DEMO-EMol was evaluated on a comprehensive benchmark set of cryo-EM maps with resolutions ranging from 1.96 to 12.77 Å, and the results demonstrated its superior performance over the state-of-the-art methods for both protein-NA and protein-protein complex modeling. The DEMO-EMol web server is freely accessible at https://zhanggroup.org/DEMO-EMol/.

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