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Proteins Structure Function and Bioinformatics
Article . 2023 . Peer-reviewed
License: CC BY
Data sources: Crossref
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PubMed Central
Other literature type . 2023
License: CC BY
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https://doi.org/10.22541/au.16...
Article . 2023 . Peer-reviewed
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Tertiary structure assessment at CASP15

Authors: Daniel Rigden; Adam Simpkin; Shahram Mesdaghi; Filomeno Sánchez Rodríguez; Luc Elliott; David Murphy; Andriy Kryshtafovych; +1 Authors

Tertiary structure assessment at CASP15

Abstract

AbstractThe results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single‐chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand‐out group, with most of the best‐scoring groups—led by PEZYFoldings, UM‐TBM, and Yang Server—employing AF2 in one way or another. Many top groups paid special attention to generating deep Multiple Sequence Alignments (MSAs) and testing variant MSAs, thereby allowing them to successfully address some of the hardest targets. Such difficult targets, as well as lacking templates, were typically proteins with few homologues. Local divergence between prediction and target correlated with localization at crystal lattice or chain interfaces, and with regions exhibiting high B‐factor factors in crystal structure targets, and should not necessarily be considered as representing error in the prediction. However, analysis of exposed and buried side chain accuracy showed room for improvement even in the latter. Nevertheless, a majority of groups produced high‐quality predictions for most targets, which are valuable for experimental structure determination, functional analysis, and many other tasks across biology. These include those applying methods similar to those used to generate major resources such as the AlphaFold Protein Structure Database and the ESM Metagenomic atlas: the confidence estimates of the former were also notably accurate.

Country
United States
Keywords

Models, Molecular, Bioinformatics, 610, Molecular, Mathematical sciences, Computational Biology, Proteins, structural bioinformatics, Biological Sciences, molecular replacement, CASP15, Mathematical Sciences, protein structure prediction, Biological sciences, machine learning, protein modelling, Models, Information and Computing Sciences, Biochemistry and Cell Biology, Furylfuramide, Sequence Alignment, Research Articles

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    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    41
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
41
Top 10%
Top 10%
Top 1%
Green
hybrid