Structure-free antibody paratope similarity prediction for in silico epitope binning via protein language models

Antibodies are an important group of biological molecules that are used as therapeutics and diagnostic tools. Although millions of antibody sequences are available, identifying their structural and functional similarity and their antigen binding sites remains a challenge at large scale. Here, we present a fast, sequence-based computational method for antibody paratope prediction based on protein language models. The paratope information is then used to measure similarity among antibodies via protein language models. Our computational method enables binning of antibody discovery hits into groups as the function of epitope engagement. We further demonstrate the utility of the method by identifying antibodies targeting highly similar epitopes of the same antigens from a large pool of antibody sequences, using two case studies: SARS CoV2 Receptor Binding Domain (RBD) and Epidermal Growth Factor Receptor (EGFR). Our approach highlights the potential in accelerating antibody discovery by enhancing hit prioritization and diversity selection.