9MSW
anti-EGFR DyAb designed FAB
Summary for 9MSW
| Entry DOI | 10.2210/pdb9msw/pdb |
| Descriptor | DyAb Fab heavy chain, DyAb Fab light chain, CHLORIDE ION, ... (5 entities in total) |
| Functional Keywords | antibody, machine learning, design, artificial intelligence, de novo, protein engineering, immune system |
| Biological source | Rattus norvegicus (rat) More |
| Total number of polymer chains | 6 |
| Total formula weight | 143687.82 |
| Authors | Kiefer, J.R.,Lin, J.Y.,Hofmann, J.L.,Watkins, A.M.,Seeger, F.,Frey, N.C.,Dou, Y.,Tang, Y. (deposition date: 2025-01-10, release date: 2026-09-09) |
| Primary citation | Lin, J.Y.,Hofmann, J.L.,Leaver-Fay, A.,Liang, W.C.,Vasilaki, S.,Lee, E.,O Pinheiro, P.,Tagasovska, N.,R Kiefer, J.,Wu, Y.,Seeger, F.,Bonneau, R.,Gligorijevic, V.,Watkins, A.,Cho, K.,Frey, N. DyAb: sequence-based antibody design and property prediction in a low-data regime. Mabs, 18:2717460-2717460, 2026 Cited by PubMed Abstract: Protein therapeutic design and property prediction are frequently hampered by data scarcity. Here we propose a model, DyAb, that addresses these issues by leveraging a pair-wise representation to predict differences in binding affinity, rather than absolute values. DyAb is built on top of a pre-trained protein language model and achieves a Spearman rank correlation of up to 0.85 on binding affinity prediction across monoclonal antibodies targeting three different antigens (EGFR, IL-6, and an internal target), given as few as 100 training data. We employ DyAb in two design contexts: as a ranking model to score combinations of known mutations, and combined with a genetic algorithm to generate new sequences. Our method consistently generates antibody variants with high binding rates, including designs that improve on the binding affinity of the lead molecule by more than ten-fold. DyAb represents a powerful tool for optimizing antibody binding affinity in low data regimes common in early-stage drug development. PubMed: 42665538DOI: 10.1080/19420862.2026.2717460 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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