Yunong Xu

StructureSAFE: A structure-aware chemical language model for unified hit identification and lead optimization

StructureSAFE is a chemical language model that combines protein structure and evolutionary information with molecular representations to improve hit identification and lead optimization, achieving state-of-the-art performance in chemical plausibility and binding affinity prediction.

3D Structure-based Generative Small Molecule Drug Design: Are We There Yet?

This paper introduces two metrics to evaluate the chemical plausibility of molecules generated by structure-based generative algorithms and compares them to virtual screening hits for three protein targets.

SLOGEN: A Structure-based Lead Optimization Model Unifying Fragment Generation and Screening

Slogen unifies fragment generation and screening for lead optimization, improving chemical diversity and synthetic tractability while matching state-of-the-art performance.

Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure

This paper investigates how epiberberine binds to a DNA quadruplex structure and shows how modifying the DNA structure enhances binding affinity, leading to a new method for extracting the compound from plant extracts.