ArticleStructure (London, England : 1993)2009
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.
Article in Structure (London, England : 1993), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.Journal of chemical theory and computation · 2026Article
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.bioRxiv : the preprint server for biology · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement.Journal of chemical information and modeling · 2025Article
- All-atom RNA structure determination from cryo-EM maps.Nature biotechnology · 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
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- 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
- Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy.Analytical chemistry · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.Structure (London, England : 1993) · 2019Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.Journal of chemical theory and computation · 2019Article
- FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.Nucleic acids research · 2018Article
- Enhanced stability of a chimeric hepatitis B core antigen virus-like-particle (HBcAg-VLP) by a C-terminal linker-hexahistidine-peptide.Journal of nanobiotechnology · 2018Article
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6 authors.
Funding
Abstract
In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.
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