ArticleJournal of structural biology2016
De Novo modeling in cryo-EM density maps with Pathwalking.
Article in Journal of structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- Seed amplification of MSA alpha-synuclein aggregates preserves the biological and structural properties of brain-derived aggregates.Nature communications · 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
- 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
- Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences.Nature communications · 2024Article
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.Bioinformatics (Oxford, England) · 2023Article
- Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements fromBiomolecules · 2023Article
- Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models.Journal of molecular biology · 2023Article
- The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.PLoS pathogens · 2023Article
- Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions.Current opinion in structural biology · 2023Review
- Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps.Biomolecules · 2022Article
- Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.International journal of molecular sciences · 2022Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB discovery · 2022Article
- 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
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Authors and funding
4 authors.
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Abstract
As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps.
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