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Sequence assignment validation in cryo-EM models with checkMySequence
Open accessPreprint — published as 10.1107/s2059798322005009 · Paper page
Abstract
The availability of new AI-based protein structure prediction tools radically changed the way cryo-EM maps are interpreted, but it has not eliminated the challenges of map interpretation faced by a microscopist. Models will continue to be locally rebuilt and refined using interactive tools. This inevitably results in occasional errors, among which register-shifts remain one of the most difficult to identify and correct. Here we introduce checkMySequence ; a fast, fully automated and parameter-free method for detecting register-shifts in protein models built into cryo-EM maps. We show that the method can assist model building in cases where poorer map resolution hinders visual interpretation. We also show that checkMySequence could have helped avoid a widely discussed sequence register error in a model of SARS-CoV-2 RNA-dependent RNA polymerase that was originally detected thanks to a visual residue-by-residue inspection by members of the structural biology community. Synopsis: We present a new method, checkMySequence , for fast and automated detection of register errors in protein models built into cryo-EM reconstructions.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Chojnowski, G.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Corresponding author
- Chojnowski, Grzegorz
- ORCID
- Chojnowski, Grzegorz
- Venue
- Acta Crystallographica Section D Structural Biology
- Publisher
- openRxiv
- Published
- 2022-01-05
- Volume
- 78
- Issue
- 7
- Pages
- 806-816
- ISSN
- 2059-7983 (ISSN-L)
- PMC
- PMC9248842
- OpenAlex
- W4281697297
- Cited by
- 20
- References
- 1
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 7 · 2023: 4 · 2022: 2
- FWCI
- 2.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Acta Crystallographica Section D Structural Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- register shift, protein structure prediction, automatic error detection
- MeSH terms
- COVID-19, SARS-CoV-2, Artificial Intelligence, Humans, Models, Molecular, Proteins, RNA, Viral, Cryoelectron Microscopy
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