Papers › Unveiling Molecular Moieties through Hierarchical Grad-CAM Graph Explainability
Unveiling Molecular Moieties through Hierarchical Grad-CAM Graph Explainability
Salvatore Contino, Paolo Sortino, Maria Rita Gulotta, Ugo Perricone, Roberto Pirrone
Background: Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (GNNs) have gained prominence for their ability to model complex molecular structures using graph-based representations. However, the integration of explainable methods to elucidate the specific contributions of molecular substructures to biological activity remains a significant challenge. This limitation hampers both the interpretability of predictive models and the rational design of novel therapeutics. Results: We trained 20 GNN models on a dataset of small molecules with the goal of predicting their activity on 20 distinct protein targets from the Kinase family. These classifiers achieved state-of-the-art performance in virtual screening tasks, demonstrating high accuracy and robustness on different targets. Building upon these models, we implemented the Hierarchical Grad-CAM graph Explainer (HGE) framework, enabling an in-depth analysis of the molecular moieties driving protein-ligand binding stabilization. HGE exploits Grad-CAM explanations at the atom, ring, and whole-molecule levels, leveraging the message-passing mechanism to highlight the most relevant chemical moieties. Validation against experimental data from the literature confirmed the ability of the explainer to recognize a molecular pattern of drugs and correctly annotate them to the known target. Conclusion: Our approach may represent a valid support to shorten both the screening and the hit discovery process. Detailed knowledge of the molecular substructures that play a role in the binding process can help the computational chemist to gain insights into the structure optimization, as well as in drug repurposing tasks.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
1 archive task tag without a task page not shown.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections