ArticleMethods (San Diego, Calif.)2016
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- Stepwise recruitment of chaperone Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibril disassembly.Communications biology · 2025Article
- Using deep-learning predictions reveals a large number of register errors in PDB depositions.IUCrJ · 2024Article
- Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.Scientific reports · 2024Article
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- Article
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote.Journal of structural biology: X · 2023Article
- CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.Proteins · 2023Article
- Structural basis of ubiquitin-independent PP1 complex disassembly by p97.The EMBO journal · 2023Article
- Structural journey of an insecticidal protein against western corn rootworm.Nature communications · 2023Article
- Using deep-learning predictions of inter-residue distances for model validation.Acta crystallographica. Section D, Structural biology · 2022Article
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution.Biomolecules · 2022Article
- Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization.The EMBO journal · 2022Article
- Structural analysis of the basal state of the Artemis:DNA-PKcs complex.Nucleic acids research · 2022Article
- Sequence-assignment validation in cryo-EM models with checkMySequence.Acta crystallographica. Section D, Structural biology · 2022Article
- Validation analysis of EMDB entries.Acta crystallographica. Section D, Structural biology · 2022Article
- Snapshots of actin and tubulin folding inside the TRiC chaperonin.Nature structural & molecular biology · 2022Article
- Atomic model validation using the CCP-EM software suite.Acta crystallographica. Section D, Structural biology · 2022Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5-4.5Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders' overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite.
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Registered trials
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.