ArticleStructure (London, England : 1993)2012
Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.
Article in Structure (London, England : 1993), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- AI-based methods for biomolecular structure modeling for Cryo-EM.Current opinion in structural biology · 2025Review
- Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.Biophysical journal · 2024Review
- Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.Bioinformatics (Oxford, England) · 2023Article
- 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
- Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera.International journal of molecular sciences · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Article
- Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM.Acta crystallographica. Section D, Structural biology · 2020Article
- Cryo-EM map interpretation and protein model-building using iterative map segmentation.Protein science : a publication of the Protein Society · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.Acta crystallographica. Section D, Structural biology · 2019Article
- De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.Journal of structural biology · 2018Article
- De novo main-chain modeling for EM maps using MAINMAST.Nature communications · 2018Article
- De Novo modeling in cryo-EM density maps with Pathwalking.Journal of structural biology · 2016Article
- Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- High resolution single particle refinement in EMAN2.1.Methods (San Diego, Calif.) · 2016Article
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5 authors.
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Abstract
A significant number of macromolecular structures solved by electron cryo-microscopy and X-ray crystallography obtain resolutions of 3.5-6Å, at which direct atomistic interpretation is difficult. To address this, we developed pathwalking, a semi-automated protocol to enumerate reasonable Cα models from near-atomic resolution density maps without a structural template or sequence-structure correspondence. Pathwalking uses an approach derived from the Traveling Salesman Problem to rapidly generate an ensemble of initial models for individual proteins, which can later be optimized to produce full atomic models. Pathwalking can also be used to validate and identify potential structural ambiguities in models generated from near-atomic resolution density maps. In this work, examples from the EMDB and PDB are used to assess the broad applicability and accuracy of our method. With the growing number of near-atomic resolution density maps from cryo-EM and X-ray crystallography, pathwalking can become an important tool in modeling protein structures.
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