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A Protocol for Computer-Based Protein Structure and Function Prediction
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Assessment of Protein Complex Predictions in CASP16: Are We Making Progress?

Jing Zhang1,2, Rongqing Yuan1,2,3, Andriy Kryshtafovych4

  • 1Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Proteins
|October 31, 2025
PubMed
Summary

Complex protein structure prediction remains challenging, with top CASP16 groups improving accuracy through advanced modeling techniques and extensive sampling. New methods show promise for difficult targets and stoichiometry prediction, highlighting areas for future research.

Keywords:
AlphaFold2AlphaFold3CASP16antigen–antibody interactionmodel samplingoligomer predictionstoichiometry

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • The Critical Assessment of Structure Prediction (CASP) benchmarks progress in protein structure prediction.
  • Multimer prediction, involving protein complexes, presents a significant computational challenge.

Purpose of the Study:

  • To assess the state of oligomer target structure prediction in CASP16.
  • To identify key trends and challenges in computational protein complex modeling.

Main Methods:

  • Analysis of results from CASP16, including standard and special phases (Phase 0 and Phase 2).
  • Evaluation of various modeling strategies, including reliance on AlphaFold-Multimer (AFM) and AlphaFold3 (AF3), MSA optimization, and massive model sampling.
  • Comparison of top-performing groups' strategies and their effectiveness.

Main Results:

  • Top groups achieved moderate accuracy improvements over CASP15, driven by AF3 and extensive sampling.
  • Optimized MSAs and refined modeling constructs significantly boosted performance beyond default AFM/AF3.
  • Alternative approaches, like those from kozakovvajda for antibody-antigen targets, showed high success rates.
  • Model ranking and stoichiometry prediction remain significant bottlenecks.

Conclusions:

  • CASP16 shows progress in multimer prediction but highlights the need for improved model ranking and stoichiometry prediction.
  • Future research should focus on developing novel modeling methods beyond current AF-based paradigms.
  • Alternative strategies show potential for specific challenging targets like antibody-antigen complexes.