ArticleJournal of molecular biology2020
A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.
Article in Journal of molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.Journal of chemical information and modeling · 2026Article
- Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.bioRxiv : the preprint server for biology · 2026Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.bioRxiv : the preprint server for biology · 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
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- Antibacterial Activity and Mechanism of Peptide PV-Q5 againstFoods (Basel, Switzerland) · 2023Article
- Ribavirin inhibits the replication of infectious bursal disease virus predominantly through depletion of cellular guanosine pool.Frontiers in veterinary science · 2023Article
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Progressive assembly of multi-domain protein structures from cryo-EM density maps.Nature computational science · 2022Article
- CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks.Nature methods · 2022Article
- Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB discovery · 2022Article
- Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps.Biomolecules · 2021Article
- EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps.Briefings in bioinformatics · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
- Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps.bioRxiv : the preprint server for biology · 2020Article
Corrections and comments
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5 authors.
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Abstract
The rapid progress of cryo-electron microscopy (cryo-EM) in structural biology has raised an urgent need for robust methods to create and refine atomic-level structural models using low-resolution EM density maps. We propose a new protocol to create initial models using I-TASSER protein structure prediction, followed by EM density map-based rigid-body structure fitting, flexible fragment adjustment and atomic-level structure refinement simulations. The protocol was tested on a large set of 285 non-homologous proteins and generated structural models with correct folds for 260 proteins, where 28% had RMSDs below 2 Å. Compared to other state-of-the-art methods, the major advantage of the proposed pipeline lies in the uniform structure prediction and refinement protocol, as well as the extensive structural re-assembly simulations, which allow for low-to-medium resolution EM density map-guided structure modeling starting from amino acid sequences. Interestingly, the quality of both the image fitting and subsequent structure refinement was found to be strongly correlated with the correctness of the initial I-TASSER models; this is mainly due to the different correlation patterns observed between force field and structural quality for the models with template modeling score (or TM-score, a metric quantifying the similarity of models to the native) above and below a threshold of 0.5. Overall, the results demonstrate a new avenue that is ready to use for large-scale cryo-EM-based structure modeling and atomic-level density map-guided structure refinement.
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