ProtAff: Protein Binding Affinity Prediction via LoRA-Finetuned ESM-2 (opens in new tab)

Predicting the binding affinity of protein--protein interactions remains a central challenge in computational biology. Structure prediction models such as AlphaFold3 (AF3) and Boltz-2 can produce high-quality docking poses, and their confidence scores indicate structure quality, but these same scores fail to rank binding affinity among confirmed binders. Here we present ProtAff, a sequence-only affinity prediction model built on ESM-2 (650M parameters) with low-rank adaptation (LoRA) fine-tun...