Health AI Central
Peer-Reviewed Publication
Molecules2025;30(23)November 22, 2025Journal Article

Systematic Exploration of Small-Molecule Binding via a Large Language Model Trained on Textualized Protein-Ligand Interactions.

Taeseob Lee1,2, Heehoon Jung1, Ahnjae Jung1,3, JaeWoong Min1, Jong Hui Hong1, Bin Claire Zhang4, Jongsun Jung1,5
1Syntekabio Inc., 18 Gukjegwahak 17-ro, Yuseong-gu, Daejeon 34002, Republic of Korea.
2Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea.
3Department of Artificial Intelligence, Korea University, Seoul 02841, Republic of Korea.
4Cerebras Systems Inc., 1237 E. Arques Ave, Sunnyvale, CA 94085, USA.
5Syntekabio USA Inc., 425 Fifth Ave. Suite 505, New York, NY 10016, USA.
PubMed PMC DOI PDF

Abstract

Emergent Large Language Models (LLMs) show impressive capabilities in performing a wide range of tasks. These models can be harnessed for biophysical use as well. The main challenge in this endeavor lies in transforming 3D chemical data into 1D language-like data. We developed a method to transform molecular data into language-like data and tokenize it for LLM use in a biophysical context. We then…

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