ArticleBriefings in bioinformatics2024
ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody-antigen computational docking.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 15 citations in OpenAlex.
- Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.Nature communications · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.Proteins · 2026Article
- Improving B-cell epitope prediction.Drug discovery today · 2025Review
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- Analysing protein complexes in plant science: insights and limitation with AlphaFold 3.Botanical studies · 2025Review
- TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.Briefings in bioinformatics · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- A comparison of antibody-antigen complex sequence-to-structure prediction methods and their systematic biases.Protein science : a publication of the Protein Society · 2024Article
- A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Accurate prediction of antibody-antigen complex structures is pivotal in drug discovery, vaccine design and disease treatment and can facilitate the development of more effective therapies and diagnostics. In this work, we first review the antibody-antigen docking (ABAG-docking) datasets. Then, we present the creation and characterization of a comprehensive benchmark dataset of antibody-antigen complexes. We categorize the dataset based on docking difficulty, interface properties and structural characteristics, to provide a diverse set of cases for rigorous evaluation. Compared with Docking Benchmark 5.5, we have added 112 cases, including 14 single-domain antibody (sdAb) cases and 98 monoclonal antibody (mAb) cases, and also increased the proportion of Difficult cases. Our dataset contains diverse cases, including human/humanized antibodies, sdAbs, rodent antibodies and other types, opening the door to better algorithm development. Furthermore, we provide details on the process of building the benchmark dataset and introduce a pipeline for periodic updates to keep it up to date. We also utilize multiple complex prediction methods including ZDOCK, ClusPro, HDOCK and AlphaFold-Multimer for testing and analyzing this dataset. This benchmark serves as a valuable resource for evaluating and advancing docking computational methods in the analysis of antibody-antigen interaction, enabling researchers to develop more accurate and effective tools for predicting and designing antibody-antigen complexes. The non-redundant ABAG-docking structure benchmark dataset is available at https://github.com/Zhaonan99/Antibody-antigen-complex-structure-benchmark-dataset.
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