-This study, introduces the Protein Ligand Binding Affinity Prediction Using Pretrained Transformers (PLAPT) model, an innovative machine learning approach to predict protein-ligand binding affinities with high accuracy and generalizability, leveraging the wide knowledge of pretrained transformer models. By using ProtBERT and ChemBERTa for encoding protein and ligand sequences, respectively, we trained a two-branch dense neural network that effectively fuses these encodings to estimate binding affinity values. The PLAPT model not only achieves a high Pearson correlation coefficient of ~0.8, but also exhibits negligible overfitting, a remarkable feat in the context of computational affinity prediction. The robustness of PLAPT, attributed to its generalized transfer learning approach from pre-trained encoders, demonstrates the substantial potential of leveraging extant biochemical knowledge to enhance predictive models in drug discovery.
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