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Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking
Open accessPreprint — published as 10.1093/bioinformatics/btae583 · Paper page
Abstract
Antibody-antigen complex modelling is an important step in computational workflows for therapeutic antibody design. While experimentally determined structures of both antibody and the cognate antigen are often not available, recent advances in machine learning-driven protein modelling have enabled accurate prediction of both antibody and antigen structures. Here, we analyse the ability of protein-protein docking tools to use machine learning generated input structures for information-driven docking. We find that HADDOCK can generate accurate models of antibodyantigen complexes using an ensemble of antibody structures generated by machine learning tools and AlphaFold2 predicted antigen structures. Targeted docking using knowledge of the complementary determining regions on the antibody and some information about the targeted epitope allows the generation of high quality models of the complex with reduced sampling, resulting in a computationally cheap protocol that outperforms the ZDOCK baseline. The data set used to benchmark the docking protocols in this study is available at github.com/haddocking/ai-antibodies. The docking models will be deposited at data.sbgrid.org/labs/32/ upon acceptance.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Giulini, M., Schneider, C., Cutting, D., Desai, N., Deane, C. M., & Bonvin, A. M. J. J.
- Affiliations
- Utrecht University (NL)
- Corresponding author
- Bonvin, Alexandre M.J.J.
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2023-11-17
- Volume
- 40
- Issue
- 10
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC11483107
- OpenAlex
- W4402984101
- Cited by
- 41
- References
- 1
- Citations by year
- 2026: 12 · 2025: 17 · 2024: 12
- FWCI
- 5.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- European Commission (823830, 101017567, 101093290)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- immune complexes, protein-protein docking, AlphaFold2, haddock, therapeutic antibody design, hypervariable region, epitope targeting, ZDOCK
- MeSH terms
- Machine Learning, Antibodies, Antigen-Antibody Complex, Epitopes, Antigens, Software, Molecular Docking Simulation
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