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TransVAE-DTA: Transformer and variational autoencoder network for drug-target binding affinity prediction

文献类型： 外文期刊

作者： Zhou, Changjian 1 ; Li, Zhongzheng 2 ; Song, Jia 2 ; Xiang, Wensheng 2 ;

作者机构： 1.Northeast Agr Univ, Sch Life Sci, Harbin, Peoples R China

2.Northeast Agr Univ, Dept Data & Comp, Harbin, Peoples R China

3.Northeast Agr Univ, Sch Engn, Harbin, Peoples R China

4.Northeast Agr Univ, Sch Plant Protect, Harbin, Peoples R China

5.Chinese Acad Agr Sci, State Key Lab Biol Plant Dis & Insect Pests, Inst Plant Protect, Beijing, Peoples R China

关键词： Drug-target binding affinity prediction; Transformer; Variational autoencoder; Drug discovery

期刊名称：COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE （ 影响因子：6.1； 五年影响因子：6.1 ）

ISSN： 0169-2607

年卷期： 2024 年 244 卷

页码：

收录情况： SCI

摘要： Background and objective: Recent studies have emphasized the significance of computational in silico drug-target binding affinity (DTA) prediction in the field of drug discovery and drug repurposing. However, existing DTA prediction approaches suffer from two major deficiencies that impede their progress. Firstly, while most methods primarily focus on the feature representations of drug-target binding affinity pairs, they fail to consider the longdistance relationships of proteins. Furthermore, many deep learning-based DTA predictors simply model the interaction of drug-target pairs through concatenation, which hampers the ability to enhance prediction performance. Methods: To address these issues, this study proposes a novel framework named TransVAE-DTA, which combines the transformer and variational autoencoder (VAE). Inspired by the early success of VAEs, we aim to further investigate the feasibility of VAEs for drug structure encoding, while utilizing the transformer architecture for target feature representation. Additionally, an adaptive attention pooling (AAP) module is designed to fuse the drug and target encoded features. Notably, TransVAE-DTA is proven to maximize the lower bound of the joint likelihood of drug, target, and their DTAs. Results: Experimental results demonstrate the superiority of TransVAE-DTA in drug-target binding affinity prediction assignments on two public Davis and KIBA datasets. Conclusions: In this research, the developed TransVAE-DTA opens a new avenue for engineering drug-target interactions.

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