ArticleActa crystallographica. Section D, Structural biology2022
Sequence-assignment validation in cryo-EM models with checkMySequence.
Article in Acta crystallographica. Section D, Structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Core-sheath coupling controls flagellar curvature and motility in Leptospira.Nature communications · 2026Article
- Architecture of an asymmetric short chain/long chain hybrid acyl‑CoA carboxylase from Mycobacterium smegmatis.Communications biology · 2026Article
- Core-sheath coupling controls flagellar curvature and motility inbioRxiv : the preprint server for biology · 2026Article
- AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage.Nucleic acids research · 2026Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Using deep-learning predictions reveals a large number of register errors in PDB depositions.IUCrJ · 2024Article
- Article
- AlphaFold two years on: Validation and impact.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages.Nature communications · 2024Article
- Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2.Nature communications · 2024Article
- Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.Nature communications · 2023Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- Sequence-assignment validation in protein crystal structure models with checkMySequence.Acta crystallographica. Section D, Structural biology · 2023Article
- Using deep-learning predictions of inter-residue distances for model validation.Acta crystallographica. Section D, Structural biology · 2022Article
- Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney.Cell discovery · 2022Article
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Authors and funding
1 author.
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Abstract
The availability of new artificial intelligence-based protein-structure-prediction tools has radically changed the way that 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, checkMySequence, a fast, fully automated and parameter-free method for detecting register shifts in protein models built into cryo-EM maps, is introduced. It is shown that the method can assist model building in cases where poorer map resolution hinders visual interpretation. It is also shown that checkMySequence could have helped to 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. The software is freely available at https://gitlab.com/gchojnowski/checkmysequence.
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