Improving drug-target affinity prediction via feature fusion and knowledge distillation

Ruiqiang Lu, Jun Wang, Pengyong Li, Yuquan Li, Shuoyan Tan, Yiting Pan, Huanxiang Liu, Peng Gao, Guotong Xie, Xiaojun Yao

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


Rapid and accurate prediction of drug-target affinity can accelerate and improve the drug discovery process. Recent studies show that deep learning models may have the potential to provide fast and accurate drug-target affinity prediction. However, the existing deep learning models still have their own disadvantages that make it difficult to complete the task satisfactorily. Complex-based models rely heavily on the time-consuming docking process, and complex-free models lacks interpretability. In this study, we introduced a novel knowledge-distillation insights drug-target affinity prediction model with feature fusion inputs to make fast, accurate and explainable predictions. We benchmarked the model on public affinity prediction and virtual screening dataset. The results show that it outperformed previous state-of-the-art models and achieved comparable performance to previous complex-based models. Finally, we study the interpretability of this model through visualization and find it can provide meaningful explanations for pairwise interaction. We believe this model can further improve the drug-target affinity prediction for its higher accuracy and reliable interpretability.

Original languageEnglish
Article numberbbad145
JournalBriefings in Bioinformatics
Issue number3
Publication statusPublished - 1 May 2023
Externally publishedYes


  • drug-target affinity prediction
  • graph neural network
  • knowledge distillation
  • virtual screening


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