Computational models in the service of X‐ray and cryo‐ electron microscopy structure determination
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Critical assessment of structure prediction (CASP) conducts community experiments to determine the state of the art in computing protein structure from amino acid sequence. The process relies on the experimental community providing information about not yet public or about to be solved structures, for use as targets. For some targets, the experimental structure is not solved in time for use in CASP. Calculated structure accuracy improved dramatically in this round, implying that models should now be much more useful for resolving many sorts of experimental difficulties. To test this, selected models for seven unsolved targets were provided to the experimental groups. These models were from the AlphaFold2 group, who overall submitted the most accurate predictions in CASP14. Four targets were solved with the aid of the models, and, additionally, the structure of an already solved target was improved. An a posteriori analysis showed that, in some cases, models from other groups would also be effective. This paper provides accounts of the successful application of models to structure determination, including molecular replacement for X‐ray crystallography, backbone tracing and sequence positioning in a cryo‐electron microscopy structure, and correction of local features. The results suggest that, in future, there will be greatly increased synergy between computational and experimental approaches to structure determination.
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AF2 models are increasingly used in X-ray crystallographic molecular replacement and phasing.
“AF2 models have also been increasingly used during molecular replacement and phasing of X-ray diffraction data obtained from protein crystals76–79”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [76]
AF models have been used extensively with single-particle cryo-EM data.
“AF models have also been used extensively together with single particle cryo-EM data60,76,95,96”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [76]
A sequence alignment error in one target experimental structure was corrected with the aid of a model.
“For example, a sequence alignment error in one of the target experimental structures was corrected with the aid of a model12.”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [12]
The structures are accurate enough to help solve structures, both X-ray and cryo-EM.
“We have already seen that the structures are accurate enough to help solve structures, both X-ray and cryo-EM12.”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [12]
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- Authors
- Kryshtafovych, A., Moult, J., Albrecht, R., Chang, G. A., Chao, K., Fraser, A., Greenfield, J., Hartmann, M. D., Herzberg, O., Josts, I., Leiman, P. G., Linden, S. B., Lupas, A. N., Nelson, D. C., Rees, S. D., Shang, X., Sokolova, M. L., Tidow, H., & AlphaFold2 team
- Affiliations
- University of California, Davis (US)
- Institute for Bioscience and Biotechnology Research (US)
- Max Planck Institute for Developmental Biology (DE)
- University of California San Diego (US)
- The University of Texas Medical Branch at Galveston (US)
- Universität Hamburg (DE)
- Skolkovo Institute of Science and Technology (RU)
- Google DeepMind (United Kingdom) (GB)
- Corresponding author
- Kryshtafovych, Andriy
- ORCID
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2021-09-06
- Volume
- 89
- Issue
- 12
- Pages
- 1633-1646
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC8616789
- OpenAlex
- W3194187547
- Cited by
- 45
- References
- 67
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 4 · 2023: 14 · 2022: 13 · 2021: 7
- FWCI
- 2.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Medical Research Council (MR/N009614/1)
- Biotechnology and Biological Sciences Research Council (BB/K01692X/1, 1350971)
- National Institute of General Medical Sciences (R01GM139034, R01GM110202, R01GM100482)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Keywords
- protein structure prediction, CASP14, AlphaFold2, molecular replacement
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Software, Crystallography, X-Ray, Computational Biology, Cryoelectron Microscopy
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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