CATransUnetLBP: Accurate Prediction of Protein-Ligand Binding Pockets Using a Hybrid Network

作者：Cheng Cai, Zhaohong Deng, Andong Li, Yun Zuo, Haoran Chen, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong‐Bin Shen, Dong‐Jun Yu · 发表于：IEEE Transactions on Computational Biology and Bioinformatics · 年份：2025 · DOI：10.1109/tcbbio.2024.3521466 · 被引用次数：1 · 研究领域：Protein Structure and Dynamics、Computational Drug Discovery Methods、Machine Learning in Bioinformatics

The development of intelligent methods capable of predicting protein-ligand binding sites has become a popular research field. Recently, deep learning based methods have been proposed as a promising solution for this task. However, some limitations still exist. For example, the network structure is not optimized for predicting protein binding pockets, which limits the model's capabilities. To address the aforementioned challenges, a novel method called CATransUnetLPB is proposed, in which a new network structure named CATransUnet is designed. The proposed CATransUnet combines CNN and Transformer models to accurately segment binding pocket regions from protein 3D structures. It outperforms existing representative methods on three test sets, demonstrating the effectiveness of optimizing the deep network model for detecting protein ligand binding pockets. Furthermore, we conduct thorough analysis on applying data augmentation to protein data structure and confirm that such technique can enhance the model's generalization ability, thereby ensuring good performance on new protein structures. Moreover, experiments show that the predicted binding pockets from our model can complement the results obtained from other methods. This suggests that integrating our method with existing approaches could further improve the prediction of protein-ligand binding pockets.