3 papers
q-bio.BM2025
Tokenizing Loops of Antibodies
Ada Fang, Robert G. Alberstein, Simon Kelow +1
The complementarity-determining regions of antibodies are loop structures that are key to their interactions with antigens, and of high importance to the design of novel biologics.…
cs.LG2025
Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks
Angelica Chen, Samuel D. Stanton, Frances Ding +6
Although large language models (LLMs) have shown promise in biomolecule optimization problems, they incur heavy computational costs and struggle to satisfy precise constraints. On…
q-bio.BM2025
Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins
Frédéric A. Dreyer, Jan Ludwiczak, Karolis Martinkus +8
We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell re…