Drug–target affinity prediction using rotary encoding and information retention mechanisms

Abstract

Drug–target affinity (DTA) prediction has been widely used in pharmaceutical research as a novel and effective method to explore the interaction strength between drugs and targets. However, existing DTA prediction models mainly rely on graphical representations of drug molecules, overlooking the intricate interactions between individual substructures. This limitation impacts both the predictive accuracy and the informational richness within the model nodes. To address these challenges, this paper proposes the Rotary Retention Graph Drug–Target Affinity (RRGDTA) network with rotation and retention mechanisms. The RRGDTA integrates an information interaction module into the extraction of drug and target features across multiple scale levels. This approach enhances the correlation within the graph representation, leading to an optimal feature representation. Furthermore, to tackle the issue of limited relationship between molecular structure and context, a Multi-Scale Interaction module (MSI) is proposed to enhance important features related to both. Additionally, to address inaccuracies in the structural features of drugs and targets, a Rotary Encoding Module (ROE) is proposed, which focuses on nearby contextual information and effectively captures the correlation between them. In order to solve the problem of insufficient information representation, an Association Prediction Module (APM) and an Intra-Mask Retention Module (IMR) are proposed to maximize the retention of drug–target information. The efficacy of the proposed RRGDTA in DTA prediction was validated on the Davis, kinase inhibitors biochemical assays (KIBA) and binding database (BindingDB) datasets. Compared with current baseline models, the proposed model achieved better results across various metrics, demonstrating its superior performance in accurate DTA prediction.