ArticleBriefings in bioinformatics2024
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- MultilevelCurrent research in structural biology · 2026Article
- AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase.International journal of molecular sciences · 2026Article
- A Novel Machine-Learning Based Method for Resolving Secondary Structure Topology in Medium-Resolution Cryo-EM Density Maps.International journal of molecular sciences · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 2026Article
- Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and AmideInternational journal of molecular sciences · 2025Article
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- DockEM: an enhanced method for atomic-scale protein-ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps.Briefings in bioinformatics · 2025Article
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
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7 authors.
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Abstract
The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems.
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