Novel molecular design via a scaffold-aware transformer with multi-scale attention mechanisms.

Authors

Junyoung Park, Sunyong Yoo

Published in

Journal of cheminformatics. Volume 18. Issue 1. May 19, 2026. Epub May 19, 2026.

Abstract

Recent advancements in artificial intelligence have demonstrated enhanced potential in accelerating drug discovery by exploring vast chemical spaces and predicting molecular properties. In particular, scaffold-constrained molecular generation has enabled the incorporation of structural constraints into the generation process. However, effectively integrating multi-scale structural information with activity-guided optimization remains challenging. To overcome these limitations, we propose a novel framework that integrates a transformer-based generative model and a graph attention network-based predictive model. The generative model produces molecules with desired structural characteristics by explicitly incorporating scaffold information, while the predictive model estimates the biological activity of the generated molecules. A supervised fine-tuning framework iteratively refines the generator through multi-stage tournament selection with experience memory. This framework guides the generator toward scaffold-consistent, high-affinity candidates while exploring novel chemical variations around a user-specified scaffold. Experimental results demonstrated that the proposed scaffold-aware transformer achieves competitive validity, uniqueness, and novelty, effectively generating novel compounds with high predicted binding affinity for biological targets. Meanwhile, an attention-based analysis extracted atom-level importance scores, highlighting the substructures that contribute to the predicted binding affinity and providing interpretable insights into structure-activity relationships. This study provides a practical and interpretable tool for scaffold-conditioned molecular generation.

PMID:
42157264
Bibliographic data and abstract were imported from PubMed on 16 Sep 2026.

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