Assessing the utility of CASP14 models for molecular replacement
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Abstract
The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real-world application. In CASP7, the metric for molecular replacement assessment involved full likelihood-based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood-based rigid-body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined log-likelihood-gain (LLG) score. This enabled multi-copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative-expected-LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X-ray, NMR or cryo-EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.
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A post-CASP study found that only two of the tested targets did not have models good enough for molecular replacement.
“A post-CASP study of the extent to which other targets could have been solved using molecular replacement by Randy Read and colleagues found that only two of those tested did not have models good enough for molecular replacement49.”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [49]
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- Authors
- Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J.
- Affiliations
- University of Cambridge (GB)
- Science and Technology Facilities Council (GB)
- University of Basel (CH)
- University of Liverpool (GB)
- Max Planck Institute for Developmental Biology (DE)
- Corresponding author
- Read, Randy J.
- ORCID
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2021-08-21
- Volume
- 89
- Issue
- 12
- Pages
- 1752-1769
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC8881082
- OpenAlex
- W3173575423
- Cited by
- 62
- References
- 47
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 13 · 2023: 17 · 2022: 15 · 2021: 11
- FWCI
- 4.25
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Science and Technology Facilities Council (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo
- Funders
- Max-Planck-Gesellschaft
- Wellcome (209407/Z/17/Z)
- Biotechnology and Biological Sciences Research Council (BB/S007105/1)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- CASP14, molecular replacement, model evaluation, rigid-body refinement, AlphaFold2, model generation, phasing, model ranking
- MeSH terms
- Algorithms, Models, Molecular, Magnetic Resonance Spectroscopy, Protein Conformation, Proteins, Software, Crystallography, X-Ray, Computational Biology
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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