ArticleACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine2018
Using Combined Features to Analyze Atomic Structures Derived from Cryo-EM Density Maps.
Article in ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy.Molecules (Basel, Switzerland) · 2020Article
- A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2019Article
- A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform.Medicines (Basel, Switzerland) · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. Many atomic structures have been derived from cryo-EM density maps of about 3Å resolution. Side-chain conformations are well determined in density maps with super-resolutions such as 1-2Å. It is desirable to have a statistical method to detect anomalous side-chains without a super-resolution density map. In this study, we analyzed structures derived from X-ray density maps with higher than 1.5Å resolution and those from cryo-EM density maps with 2-4 Å and 4-6 Å resolutions respectively. We introduce a histogram-based outlier score (HBOS) for anomaly detection in protein models built from cryo-EM density maps. This method uses the statistics derived from X-ray dataset (<1.5Å) as the reference and combines five features involving the distal block distance, side-chain length, phi, psi, and first chi angle of the residue. Higher percentages of anomalies were observed in the cryo-EM models than in the super-resolution X-ray models. Lower percentages of anomalies were observed in cryo-EM models derived after January 2017 than those derived before 2017.
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Registered trials
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