Improved antibody-specific epitope prediction using AlphaFold and AbAdapt
Open accessPreprint — published as 10.1002/cbic.202200303
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 assess the impact of integrating the state-of-the-art protein modeling method AlphaFold with the AbAdapt pipeline and demonstrate significant improvement in the prediction of antibody-specific epitope residues.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Antibody structure prediction using interpretable deep learning
Ruffolo, J. A., Sulam, J., & Gray, J. J. (2022) · Patterns · doi:10.1016/j.patter.2021.100406 · Cited by 216 · see citing works
Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro
Ghani, U., Desta, I., Jindal, A., Khan, O., Jones, G., Hashemi, N., Kotelnikov, S., Padhorny, D., Vajda, S., & Kozakov, D. (2021) · doi:10.1101/2021.09.07.459290 · Cited by 68 · see citing works
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- Authors
- Xu, Z., Davila, A., Wiamowski, J., Teraguchi, S., & Standley, D. M.
- Affiliations
- Research Institute for Microbial Diseases, The University of Osaka (JP)
- Shiga University (JP)
- Corresponding author
- Standley, Daron M.
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2022-05-22
- OpenAlex
- W4281295051
- Cited by
- 4
- References
- 3
- Citations by year
- 2024: 2 · 2023: 1 · 2022: 1
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- OUKA (Osaka University Knowledge Archive) (Osaka University) (submittedVersion)
- Funders
- Japan Agency for Medical Research and Development (22ama121025j0001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- epitope prediction, antibody-antigen binding, AlphaFold, rigid docking, binding site prediction
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