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Sequence-assignment validation in protein crystal structure models with checkMySequence
Open accessPublished version of a preprint
Abstract
Sequence-register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication, it was shown that register shifts in cryo-EM models of proteins can be detected using a systematic reassignment of short model fragments to the target sequence. Here, it is shown that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias-corrected electron-density maps (2 mF o − DF c ). Five register-shift errors in models deposited in the PDB detected using this method are described in detail.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549
Accelerating crystal structure determination with iterative AlphaFold prediction
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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
- Published
- 2023-06-14
- Volume
- 79
- Issue
- 7
- Pages
- 559-568
- ISSN
- 2059-7983 (ISSN-L)
- PMC
- PMC10306063
- OpenAlex
- W4380575664
- Cited by
- 5
- References
- 3
- Citations by year
- 2025: 3 · 2024: 2
- FWCI
- 0.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- 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 › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Keywords
- model validation, electron density maps, model bias correction
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Cryoelectron Microscopy, Macromolecular Substances
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