ArticleJournal of computational biology : a journal of computational molecular cell biology2017
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- DeepSSETracer 2.0: Improved Deep Learning Model Performance for Protein Secondary Structure Segmentation from Cryo-EM Maps.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
- Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB discovery · 2022Article
- Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps.Biomolecules · 2021Article
- Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps.Journal of chemical information and modeling · 2020Article
- A Pattern Recognition Tool for Medium-resolution Cryo-EM Density Maps and Low-resolution Cryo-ET Density maps.Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China) · 2018Article
- Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.Molecules (Basel, Switzerland) · 2018Article
- Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.BioMed research international · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.
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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.