TrGPCR: GPCR–Ligand Binding Affinity Prediction Based on Dynamic Deep Transfer Learning

Predicting G protein-coupled receptor (GPCR) -ligand binding affinity plays a crucial role in drug development. However, determining GPCR-ligand binding affinities is time-consuming and resource-intensive. Although many studies used data-driven methods to predict binding affinity, most of these methods required protein 3D structure, which was often unknown. Moreover, part of these studies only considered the sequence characteristics of the protein, ignoring the secondary structure of the protein. The number of known GPCR for affinity prediction is only a few thousand, which is insufficient for deep learning training. Therefore, this study aimed to propose a deep transfer learning method called TrGPCR, which used dynamic transfer learning to solve the problem of insufficient GPCR data. We used the Binding Database (BindingDB) as the source domain and the GLASS (GPCR-Ligand Association) database as the target domain. We also introduced protein secondary structures, called pockets, as features to predict binding affinities. Compared with DeepDTA, our model improved by 5.2% on RMSE (root mean square error) and 4.5% on MAE (mean squared error).