ArticleProtein science : a publication of the Protein Society2018
Guidelines for using Bsoft for high resolution reconstruction and validation of biomolecular structures from electron micrographs.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 citing papers in PubMed.
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- P-type ATPase magnesium transporter MgtA acts as a dimer.Nature structural & molecular biology · 2025Article
- Review
- The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1-17).Nucleic acids research · 2025Article
- CryoEM and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions.The FEBS journal · 2025Article
- Structural insights into the high basal activity and inverse agonism of the orphan receptor GPR6 implicated in Parkinson's disease.Science signaling · 2024Article
- Paenilamicins are context-specific translocation inhibitors of protein synthesis.Nature chemical biology · 2024Article
- The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.Nucleic acids research · 2024Article
- Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer.Journal of structural biology · 2024Article
- The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAbioRxiv : the preprint server for biology · 2024Article
- Paenilamicins from the honey bee pathogenbioRxiv : the preprint server for biology · 2024Article
- CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.Scientific reports · 2024Article
- The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome.Nature communications · 2024Article
- RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.Nature communications · 2024Article
- DNA-origami-directed virus capsid polymorphism.Nature nanotechnology · 2023Article
- Structural basis for translation inhibition by the glycosylated drosocin peptide.Nature chemical biology · 2023Article
- Structural genomics of the human dopamine receptor system.Cell research · 2023Article
17 more citing papers are in PubMed but not listed here.
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Abstract
Cryo-electron microscopy (cryoEM) is becoming popular as a tool to solve biomolecular structures with the recent availability of direct electron detectors allowing automated acquisition of high resolution data. The Bsoft software package, developed over 20 years for analyzing electron micrographs, offers a full workflow for validated single particle analysis with extensive functionality, enabling customization for specific cases. With the increasing use of cryoEM and its automation, proper validation of the results is a bigger concern. The three major validation approaches, independent data sets, resolution-limited processing, and coherence testing, can be incorporated into any Bsoft workflow. Here, the main workflow is divided into four phases: (i) micrograph preprocessing, (ii) particle picking, (iii) particle alignment and reconstruction, and (iv) interpretation. Each of these phases represents a conceptual unit that can be automated, followed by a check point to assess the results. The aim in the first three phases is to reconstruct one or more validated maps at the best resolution possible. Map interpretation then involves identification of components, segmentation, quantification, and modeling. The algorithms in Bsoft are well established, with future plans focused on ease of use, automation and institutionalizing validation.
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