4 papers
SpecOpt: Contact-Diff Reasoning for Agentic Molecule Optimization Toward Binding Specificity
Thao Nguyen, Heng Ji
Off-target protein binding is a major source of adverse effects for small-molecule drugs, yet most structure-based molecular design methods focus on generating selective compounds…
EnSol: an environment-aware graph neural network for molecular solubility prediction
Thao Nguyen, Saman Shafaei, Zhengyi Zhang +2
Molecular solubility directly affects key aspects of molecular development such as reaction feasibility, formulation performance, separation efficiency, and solvent selection. Howe…
Fraglingo: Molecular Design via Attachment-Aware Autoregressive Fragment Generation
Thao Nguyen, Jeonghwan Kim, Zhenhailong Wang +1
We introduce Fraglingo, an autoregressive molecular generator that constructs molecules step by step from chemically meaningful fragments connected through predefined attachment si…
FARM: Enhancing Molecular Representations with Functional Group Awareness
Thao Nguyen, Kuan-Hao Huang, Ge Liu +3
We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular…