Simpkin, Adam J, Sanchez Rodriguez, Filomeno, Mesdaghi, Shahram, Kryshtafovych, Andriy and Rigden, Daniel J 
ORCID: 0000-0002-7565-8937
(2021)
Evaluation of model refinement in CASP14.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89 (12).
pp. 1852-1869.
Abstract
We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely. Overall, only four groups out-performed a "naïve predictor" corresponding to the resubmission of the starting model. Among the top groups, there are interesting differences of approach and in the spread of improvements seen: some methods are more conservative, others more adventurous. Some targets were "double-barreled" for which predictors were offered a high-quality AlphaFold 2 (AF2)-derived prediction alongside another of lower quality. The AF2-derived models were largely unimprovable, many of their apparent errors being found to reside at domain and, especially, crystal lattice contacts. Refinement is shown to have a mixed impact overall on structure-based function annotation methods to predict nucleic acid binding, spot catalytic sites, and dock protein structures.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | CASP, function prediction, refinement, structure prediction |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 23 Sep 2021 15:03 |
| Last Modified: | 18 Jan 2023 21:28 |
| DOI: | 10.1002/prot.26185 |
| Open Access URL: | https://doi.org/10.1002/prot.26185 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3138060 |
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