ArticleProteins2026
AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.
Article in Proteins, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed.
- Biomolecular Interaction Prediction in the Pre- and Post-AlphaFold Era: The 8th CAPRI Evaluation.Proteins · 2026Article
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition.bioRxiv : the preprint server for biology · 2026Article
- Structural insights into clonal restriction and diversity in T cell recognition of two immunodominant SARS-CoV-2 nucleocapsid epitopes.Nature communications · 2025Article
- Evaluation of AlphaFold modeling for elucidation of nanobody-peptide epitope interactions.The Journal of biological chemistry · 2025Article
- Evaluation of Alphafold modeling for elucidation of nanobody-peptide epitope interactions.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Accurate modeling of the structures of protein-protein complexes and other biomolecular interactions represents a longstanding and important challenge for computational biology. The Critical Assessment of PRedicted Interactions (CAPRI) experiment has served for over two decades as a key means to assess and compare current approaches and methods through blind predictive scenarios, highlighting useful strategies, and new developments. Here we describe the performance of our laboratory's team in recent CAPRI rounds, which included submissions for 10 modeling targets. Our team utilized a range of docking and modeling approaches, including ZDOCK, Rosetta, and ZRANK, to model, refine, and score protein-protein and protein-DNA complexes. For recent targets we utilized adaptations of AlphaFold to generate models, leading to near-native models for an antibody-peptide target, and a highly accurate (but low ranked) model for an antibody-MHC complex. These results underscore the utility of AlphaFold-based protocols for predictive protein complex modeling, including for immune recognition, and highlight considerations regarding the use of AlphaFold confidence metrics in model selection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.