TF-DTA: A Deep Learning Approach Using Transformer Encoder to Predict Drug-Target Binding Affinity

Bioinformatics is a rapidly growing field that involves the application of computational methods to analyze and interpret biological data. One important task in bioinformatics is predicting the drug-target affinity (DTA), which plays a significant role in drug discovery through virtual screening. Effectively predicting the association between drug molecules and target molecules can speed up the drug discovery process. The DTA can be quantitatively measured. This quantifiable affinity is more precise than a simple binary relationship. In this study, we propose a deep learning model for DTA prediction that utilizes the encoder module of the Transformer architecture. Our proposed model utilizes Convolutional Neural Networks (CNNs) and the encoder module of Transformer to characterize protein and drug sequences. The model outperforms some methods such as KronRLS, SimBoost and DeepDTA as evidenced by superior evaluation metrics such as Mean Squared Error (MSE), Concordance Index (CI), and Regression toward the Mean Index $\left( {r_m^2} \right)$. These results demonstrate the effectiveness of the Transformer’s encoder in extracting meaningful representations from sequences, thereby improving the accuracy of DTA prediction. Deep learning models for DTA prediction can accelerate drug discovery by identifying drug candidates with high binding affinity to specific targets. Compared to traditional methods, the use of machine learning technology enables more effective and efficient drug discovery.