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Tertiary structure assessment at CASP15
  • +5
  • Daniel Rigden,
  • Adam Simpkin,
  • Shahram Mesdaghi,
  • Filomeno Sánchez Rodríguez,
  • Luc Elliott,
  • David Murphy,
  • Andriy Kryshtafovych,
  • Ronan Keegan
Daniel Rigden
University of Liverpool Institute of Systems Molecular and Integrative Biology

Corresponding Author:drigden@liverpool.ac.uk

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Adam Simpkin
University of Liverpool Institute of Systems Molecular and Integrative Biology
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Shahram Mesdaghi
University of Liverpool Institute of Systems Molecular and Integrative Biology
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Filomeno Sánchez Rodríguez
University of Liverpool Institute of Systems Molecular and Integrative Biology
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Luc Elliott
University of Liverpool Institute of Systems Molecular and Integrative Biology
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David Murphy
University of Liverpool Institute of Systems Molecular and Integrative Biology
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Andriy Kryshtafovych
University of California Davis Genome Center
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Ronan Keegan
Rutherford Appleton Laboratory
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Abstract

The results of tertiary structure assessment at CASP15 are reported. For the first time, recognising 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: small size, high α-helical content and monomeric structure were other likely aggravating factors. Local divergence between prediction and target correlated with localisation at crystal lattice or chain interfaces, and with regions exhibiting high B-factor factors in crystal structure targets, but 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, including those applying methods similar to those used to generate major resources such as the AlphaFold Protein Structure Database and the ESM Metagenomic atlas, produced high quality predictions for most targets which are valuable for experimental structure determination, functional analysis and many other tasks across biology.
24 May 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
24 May 2023Submission Checks Completed
24 May 2023Assigned to Editor
24 May 2023Review(s) Completed, Editorial Evaluation Pending
01 Jun 2023Reviewer(s) Assigned
14 Aug 2023Editorial Decision: Revise Minor
26 Aug 20231st Revision Received
26 Aug 2023Submission Checks Completed
26 Aug 2023Assigned to Editor
26 Aug 2023Review(s) Completed, Editorial Evaluation Pending
07 Sep 2023Editorial Decision: Accept