ArticleNature methods2015
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 225 papers.
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Who cites it
225 citing papers in PubMed.
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- Beyond Classical Force Fields: Physics-Driven Assessment of the Grappa Machine-Learned Force Field on the FoldBind Dataset.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.bioRxiv : the preprint server for biology · 2026Article
- Structural insight into the assembly and D antigenicity of polio type 1 stabilized virus-like particles.NPJ vaccines · 2026Article
- Designability of α-Helical Protein Filaments.Sub-cellular biochemistry · 2026Review
- Direct calculation of variable-resolution maps by fully analytic approximations to atomic images.Journal of applied crystallography · 2025Article
- Oligomeric HIV-1 integrase structures reveal functional plasticity for intasome assembly and RNA binding.Nature communications · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- Local structural flexibility drives oligomorphism in computationally designed protein assemblies.Nature structural & molecular biology · 2025Article
- The conformational landscape of TRiC ring-opening and its underlying stepwise mechanism revealed by cryo-EM.QRB discovery · 2025Article
- Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics.Cancer biology & therapy · 2024Article
- Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.Immunity · 2024Article
- Multifocal, multiphenotypic tumours arising from an MTOR mutation acquired in early embryogenesis.Oncogene · 2024Article
- Vaccine Potency and Structure of Yeast-Produced Polio Type 2 Stabilized Virus-like Particles.Vaccines · 2024Article
- High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector.Journal of structural biology · 2024Article
- Isolation of human antibodies against influenza B neuraminidase and mechanisms of protection at the airway interface.Immunity · 2024Article
- Structure and design of Langya virus glycoprotein antigens.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector.bioRxiv : the preprint server for biology · 2024Article
- DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting.Briefings in bioinformatics · 2024Article
- Conventional Electron Microscopy, Cryogenic Electron Microscopy, and Cryogenic Electron Tomography of Viruses.Sub-cellular biochemistry · 2024Review
165 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.