ArticleChembiochem : a European journal of chemical biology2022
Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.
Article in Chembiochem : a European journal of chemical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The Ratio of Immunogenicity: A quantitative metric to identify highly immunogenic protein antigens to improve tissue-engineered biomaterials.Biomaterials · 2026Article
- Artificial intelligence in immunotherapy: revolutionizing diagnostic and therapeutic applications in cancer and autoimmune diseases.Clinical and experimental medicine · 2026Review
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- Improving B-cell epitope prediction.Drug discovery today · 2025Review
- AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.Science advances · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Computational electrostatic engineering of nanobodies for enhanced SARS-CoV-2 receptor binding domain recognition.Frontiers in molecular biosciences · 2025Article
- Review
- Engineering therapeutic monoclonal antibodies.The Journal of allergy and clinical immunology · 2024Review
- Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.Briefings in bioinformatics · 2024Article
- Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences.mSystems · 2023Article
- Simplifying complex antibody engineering using machine learning.Cell systems · 2023Review
- Recent Progress in Antibody Epitope Prediction.Antibodies (Basel, Switzerland) · 2023Review
- SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs.Nucleic acids research · 2023Article
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug discovery today · 2023Review
- Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.Chembiochem : a European journal of chemical biology · 2022Article
- A new dawn for monoclonal antibodies against antimicrobial resistant bacteria.Frontiers in microbiology · 2022Review
- Advances in antibody discovery from human BCR repertoires.Frontiers in bioinformatics · 2022Review
- Article
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Authors and funding
5 authors.
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Abstract
Antibodies recognize their cognate antigens with high affinity and specificity, but the prediction of binding sites on the antigen (epitope) corresponding to a specific antibody remains a challenging problem. To address this problem, we developed AbAdapt, a pipeline that integrates antibody and antigen structural modeling with rigid docking in order to derive antibody-antigen specific features for epitope prediction. In this study, we systematically assessed the impact of integrating the state-of-the-art protein modeling method AlphaFold with the AbAdapt pipeline. By incorporating more accurate antibody models, we observed improvement in docking, paratope prediction, and prediction of antibody-specific epitopes. We further applied AbAdapt-AF in an anti-receptor binding domain (RBD) antibody complex benchmark and found AbAdapt-AF outperformed three alternative docking methods. Also, AbAdapt-AF demonstrated higher epitope prediction accuracy than other tested epitope prediction tools in the anti-RBD antibody complex benchmark. We anticipate that AbAdapt-AF will facilitate prediction of antigen-antibody interactions in a wide range of applications.
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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.