AntiFold: improved structure-based antibody design using inverse folding

Journal article

Summary: The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining structural integrity during antibody design. Here, we present AntiFold, an antibody-specific inverse folding model, fine-tuned from ESM-IF1 on solved and predicted antibody structures. AntiFold outperforms existing inverse folding tools on sequence recovery across complementarity-determining regions, with designed sequences showing high structural similarity to their solved counterpart. It additionally achieves stronger correlations when predicting antibody-antigen binding affinity in a zero-shot manner. AntiFold assigns low probabilities to mutations that disrupt antigen binding, synergizing with protein language model residue probabilities, and demonstrates promise for guiding antibody optimization while retaining structure-related properties. Availability and implementation: AntiFold is freely available under the BSD 3-Clause as a web server (https://opig.stats.ox.ac.uk/webapps/antifold/) and pip-installable package (https://github.com/oxpig/AntiFold).

Authors: Høie, MH; Hummer, AM; Olsen, TH; Aguilar-Sanjuan, B; Nielsen, M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Bioinformatics Advances
• Volume: 5
• Issue: 1
• Article number: vbae202
• Publication date: 2025-03-21
• Acceptance date: 2025-03-19
• DOI: 10.1093/bioadv/vbae202
• EISSN: 2635-0041
• ISSN: 2635-0041
• Language: English