ArticleNucleic acids research2025
DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- MultilevelCurrent research in structural biology · 2026Article
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase.International journal of molecular sciences · 2026Article
- Improving the Reliability of Protein Folding Rate Predictions by Applying Guidelines for Validating QSAR/QSPR Models.International journal of molecular sciences · 2026Article
- When cryo-EM modeling meets structure prediction.Nature structural & molecular biology · 2026Article
- ACGA a Novel Biomimetic Hybrid Optimisation Algorithm Based on a HP Protein Visualizer: An Interpretable Web-Based Tool for 3D Protein Folding Based on the Hydrophobic-Polar Model.Biomimetics (Basel, Switzerland) · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
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6 authors.
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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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