Health AI Central
Peer-Reviewed Publication
J Chem Inf Model2026July 16, 2026Journal Article

LINKER: Learning Interactions between Functional Groups and Residues with Chemical Knowledge-Enhanced Reasoning and Explainability.

Phuc Pham1, Viet Thanh Duy Nguyen1, Kevin Song2, Jake Chen3, Truong-Son Hy1
1Department of Computer Science, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States.
2Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States.
3Department of Biomedical Informatics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States.
PubMed DOI

Abstract

Accurate identification of interactions between protein residues and ligand functional groups is critical for understanding molecular recognition and guiding rational drug design. Existing deep learning approaches for protein-ligand interpretability typically rely on three-dimensional structural input or distance-based contact labels, which limit both their applicability and biological relevance.…

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