2025Zhang Emol

Citation

Z. Zhang, L. Xu, S. Zhang, C. Peng, G. Zhang, and X. Zhou, “EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation,” Nucleic Acids Research, p. gkaf416, 2025.

Abstract

Atomic str uct ure modeling is a cr ucial step in determining the str uct ures of protein comple x es using cry o-electron microscop y (cry o-EM). T his work introduces DEMO-EMol, an improved server that integrates deep learning-based map segmentation and chain fitting to accurately assem- ble protein–nucleic acid (NA) complex str uct ures from cryo-EM density maps. Starting from a density map and independently modeled chain str uct ures, 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, f ollo w ed b y domain-le v el fitting and optimization f or protein chains. The output of DEMO-EMol includes the final assembled complex model along with overall and residue-level quality assessments. DEMO-EMol w as e v aluated 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/ .

Links

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf416/8131116