ArticleNature computational science2022
Progressive assembly of multi-domain protein structures from cryo-EM density maps.
Article in Nature computational science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 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
- EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba.Nature communications · 2026Article
- Improving the Reliability of Protein Folding Rate Predictions by Applying Guidelines for Validating QSAR/QSPR Models.International journal of molecular sciences · 2026Article
- Structure-activity relationship of prevalent synthetic cannabinoid metabolites on hCBActa pharmacologica Sinica · 2026Article
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- Advances in Crystallography and Cryo-Electron Microscopy for the Study of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues.Fundamental research · 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
- Unraveling the Obesogenic Mechanism of Bisphenol A Through Network Toxicology and Molecular Docking: Identification of Key Molecular Targets.International journal of molecular sciences · 2025Article
- Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and AmideInternational journal of molecular sciences · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 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
- Review
- All-atom RNA structure determination from cryo-EM maps.Nature biotechnology · 2025Article
- Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation.Bioinformatics advances · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.Nature communications · 2024Article
- Structural Characterization of Heat Shock Protein 90β and Molecular Interactions with Geldanamycin and Ritonavir: A Computational Study.International journal of molecular sciences · 2024Article
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6 authors.
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Abstract
Progress in cryo-electron microscopy has provided the potential for large-size protein structure determination. However, the success rate for solving multi-domain proteins remains low because of the difficulty in modelling inter-domain orientations. Here we developed domain enhanced modeling using cryo-electron microscopy (DEMO-EM), an automatic method to assemble multi-domain structures from cryo-electron microscopy maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep-neural-network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to 12 continuous and discontinuous domains with medium- to low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (template modeling score (TM-score) >0.5) for 97% of cases and outperformed state-of-the-art methods. DEMO-EM was applied to the severe acute respiratory syndrome coronavirus 2 genome and generated models with average TM-score and root-mean-square deviation of 0.97 and 1.3 Å, respectively, with respect to the deposited structures. These results demonstrate an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modelling from cryo-electron microscopy maps.
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