4 papers
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.…
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…
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…
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms
Samuel Stanton, Robert Alberstein, Nathan Frey +2
There is a growing body of work seeking to replicate the success of machine learning (ML) on domains like computer vision (CV) and natural language processing (NLP) to applications…