Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)

R. Dustin Schaeffer, Lisa Kinch, Andriy Kryshtafovych, Nick V. Grishin

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

The high accuracy of some CASP14 models at the domain level prompted a more detailed evaluation of structure predictions on whole targets. For the first time in critical assessment of structure prediction (CASP), we evaluated accuracy of difficult domain assembly in models submitted for multidomain targets where the community predicted individual evaluation units (EUs) with greater accuracy than full-length targets. Ten proteins with domain interactions that did not show evidence of conformational change and were not involved in significant oligomeric contacts were chosen as targets for the domain interaction assessment. Groups were ranked using complementary interaction scores (F1, QS score, and Jaccard coefficient), and their predictions were evaluated for their ability to correctly model inter-domain interfaces and overall protein folds. Target performance was broadly grouped into two clusters. The first consisted primarily of targets containing two EUs wherein predictors more broadly predicted domain positioning and interfacial contacts correctly. The other consisted of complex two-EU and three-EU targets where few predictors performed well. The highest ranked predictor, AlphaFold2, produced high-accuracy models on eight out of 10 targets. Their interdomain scores on three of these targets were significantly higher than all other groups and were responsible for their overall outperformance in the category. We further highlight the performance of AlphaFold2 and the next best group, BAKER-experimental on several interesting targets.

Original languageEnglish (US)
Pages (from-to)1700-1710
Number of pages11
JournalProteins: Structure, Function and Bioinformatics
Volume89
Issue number12
DOIs
StatePublished - Dec 2021

Keywords

  • CASP14
  • classification
  • fold space
  • protein domains
  • protein structure
  • protein–protein interactions
  • sequence homologs multidomain proteins
  • structure prediction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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