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Towards a greener AlphaFold2 protocol for antibody-antigen modeling: Insights from CAPRI Round 55
Open accessPreprint — published as 10.1002/prot.26820 · Paper page
Abstract
In the 55 th round of CAPRI, we used enhanced AlphaFold2 (AF2) sampling and data-driven docking. Our AF2 protocol relies on Wallner’s massive sampling approach, which combines different AF2 versions and sampling parameters to produce thousands of models per target. For T231 (an antibody peptide complex) and T232 (PP2A:TIPRL complex), we employed a 50-fold reduced MinnieFold sampling and a custom ranking approach, leading to a top-ranking medium prediction in both cases. For T233 and T234 (two antibody bound MHC I complexes), we followed data-driven docking, which did not lead to an acceptable model. Our post-CAPRI55 analysis showed that if we would have used our MinnieFold approach on T233 and T234, we could have submitted a medium-quality model for T233 as well. In the scoring challenge, we utilized the scoring function of FoldX, which was effective in selecting acceptable models for T231 and medium quality models for T232. Our success, especially in predicting and ranking a medium quality model for T231 and potentially for T233 underscores the feasibility of green and accurate enhanced AF2 sampling in antibody complex prediction.
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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
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Research works printed but not linked: 25
- 10.1101/2021.10.04.463034 · DOI · Paper page
- 10.1002/prot.26598 · DOI · Paper page
- 10.1002/prot.26569 · DOI · Paper page
- 10.1002/prot.26562 · DOI · Paper page
- 10.1093/bioinformatics/btad573 · DOI · Paper page
- 10.1002/prot.26609 · DOI
- 10.1093/nar/gki387 · DOI · Paper page
- 10.1038/s41592-022-01488-1 · DOI · Paper page
- 10.1038/s41586-024-07487-w · DOI · Paper page
- 10.1038/s41596-024-01011-0 · DOI
- 10.1103/PhysRevLett.129.238101 · DOI · Paper page
- 10.1002/jcc.20291 · DOI
- 10.1002/jcc.21287 · DOI
- McLachlan A.D , Rapid Comparison of Protein Structres. Acta Cryst A38, 871-873. 1982. as implemented in the program ProFit (Martin, A.C.R. and Porter, C.T., http://www.bioinf.org.uk/software/profit/) · DOI
- 10.12688/f1000research.17456.1 · DOI
- 10.1101/2024.05.28.596225 · DOI
- 10.1016/j.jmb.2024.168649 · DOI
- 10.1038/s41467-017-02405-3 · DOI · Paper page
- 10.1042/BST20210410 · DOI
- 10.3389/fimmu.2017.00292 · DOI
- 10.4049/jimmunol.172.10.6175 · DOI
- 10.1126/science.aao5154 · DOI
- 10.1002/pro.4865 · DOI · Paper page
- 10.1038/s43588-024-00714-4 · DOI · Paper page
- Raouraoua N , Lensink M , Brysbaert G. Massive sampling strategy for antibody-antigen targets in CAPRI Round 55 with MassiveFold. Authorea. Published online August 25, 2021. Accessed December 23, 2024. https://www.authorea.com/users/829821/articles/1223804-massive-sampling-strategy-for-antibody-antigen-targets-in-capri-round-55-with-massivefold · DOI
Metadata
- Authors
- Savaş, B., Yılmazbilek, İ., Özsan, A., & Karaca, E.
- Affiliations
- Dokuz Eylül University (TR)
- Izmir Biomedicine and Genome Center (TR)
- Corresponding author
- Karaca, Ezgi
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- openRxiv
- Published
- 2024-10-11
- Volume
- 94
- Issue
- 11
- Pages
- 1851-1857
- ISSN
- 0887-3585 (ISSN-L)
- OpenAlex
- W4408161620
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 1 · 2025: 3
- FWCI
- 1.21
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- European Molecular Biology Organization
- Türkiye Bilimsel ve Teknolojik Araştırma Kurumu
- 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
- AlphaFold2, enhanced sampling, antibody-peptide complex, model ranking
- MeSH terms
- Antibodies, Antigen-Antibody Complex, Models, Molecular, Protein Conformation, Software, Computational Biology, Molecular Docking Simulation
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