ArticleJournal of structural biology2012
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.
Article in Journal of structural biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.PLoS computational biology · 2023Article
- Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution.Frontiers in molecular biosciences · 2021Article
- Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Cryo_fit: Democratization of flexible fitting for cryo-EM.Journal of structural biology · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.Bioscience reports · 2017Review
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
- Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.Methods (San Diego, Calif.) · 2016Article
- Validation methods for low-resolution fitting of atomic structures to electron microscopy data.Archives of biochemistry and biophysics · 2015Article
- Article
- Collective variable approaches for single molecule flexible fitting and enhanced sampling.Chemical reviews · 2014Review
- Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.Journal of structural biology · 2014Article
- Computational methods for constructing protein structure models from 3D electron microscopy maps.Journal of structural biology · 2013Article
- Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking.Biochemistry · 2013Article
- Cryo-electron microscopy--a primer for the non-microscopist.The FEBS journal · 2013Review
- Go hybrid: EM, crystallography, and beyond.Current opinion in structural biology · 2012Review
- Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.The journal of physical chemistry. B · 2012Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
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4 authors.
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Abstract
Cryo-elecron microscopy (cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map. A commonly used protocol for accommodating the conformational changes between the X-ray structure and the cryo-EM map is rigid body fitting of individual domains. With the emergence of different flexible fitting approaches, there is a need to compare and revise these different protocols for the fitting. We have applied three diverse automated flexible fitting approaches on a protein dataset for which rigid domain fitting (RDF) models have been deposited in the PDB. In general, a consensus is observed in the conformations, which indicates a convergence from these theoretically different approaches to the most probable solution corresponding to the cryo-EM map. However, the result shows that the convergence might not be observed for proteins with complex conformational changes or with missing densities in cryo-EM map. In contrast, RDF structures deposited in the PDB can represent conformations that not only differ from the consensus obtained by flexible fitting but also from X-ray crystallography. Thus, this study emphasizes that a "consensus" achieved by the use of several automated flexible fitting approaches can provide a higher level of confidence in the modeled configurations. Following this protocol not only increases the confidence level of fitting, but also highlights protein regions with uncertain fitting. Hence, this protocol can lead to better interpretation of cryo-EM data.
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