ArticleJournal of structural biology2018
Single particle reconstruction and validation using Bsoft for the map challenge.
Article in Journal of structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Structural basis of selective cannabinoid CBNature communications · 2023Article
- Structure insights into selective coupling of G protein subtypes by a class B G protein-coupled receptor.Nature communications · 2022Article
- Molecular insights into the distinct signaling duration for the peptide-induced PTH1R activation.Nature communications · 2022Article
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Article
- Bsoft: Image Processing for Structural Biology.Bio-protocol · 2022Article
- Identification and mechanism of G protein-biased ligands for chemokine receptor CCR1.Nature chemical biology · 2022Article
- Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7.Science (New York, N.Y.) · 2022Article
- Structural basis of GABANature · 2021Article
- High resolution electron tomography and segmentation-by-modeling interpretation in Bsoft.Protein science : a publication of the Protein Society · 2021Article
- Structural basis for activation of the growth hormone-releasing hormone receptor.Nature communications · 2020Article
- Cryo-EM structures of inactive and active GABACell research · 2020Article
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
- Protocols for Processing and Interpreting cryoEM Data Using Bsoft: A Case Study of the Retinal Adhesion Protein, Retinoschisin.Bio-protocol · 2020Article
- Structures and operating principles of the replisome.Science (New York, N.Y.) · 2019Article
- Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Comparing cryo-EM structures.Journal of structural biology · 2018Article
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Authors and funding
1 author.
Funding
Abstract
The Bsoft package is aimed at processing electron micrographs for the determination of the three-dimensional structures of biological specimens. Recent advances in hardware allow us to solve structures to near atomic resolution using single particle analysis (SPA). The Map Challenge offered me an opportunity to test the ability of Bsoft to produce reconstructions from cryo-electron micrographs at the best resolution. I also wanted to understand what needed to be done to work towards full automation with validation. Here, I present two cases for the Map Challenge using Bsoft: ß-galactosidase and GroEL. I processed two independent subsets in each case with resolution-limited alignment. In both cases the reconstructions approached the expected resolution within a few iterations of alignment. I further validated the results by coherency-testing: i.e., that the reconstructions from real particles give better resolutions than reconstructions from the same number of aligned noise images. The key operations requiring attention for full automation are: particle picking, faster accurate alignment, proper mask generation, appropriate map sharpening, and understanding the amount of data needed to reach a desired resolution.
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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.