8 papers
MoleCode unlocks structural intelligence in large language models
Zhiyuan Yan, Chen Liu, Boxuan Zhao +8
Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses…
End-to-End Reverse Screening Identifies Protein Targets of Small Molecules Using HelixFold3
Shengjie Xu, Xianbin Ye, Mengran Zhu +3
Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and…
Reshaping Biomolecular Structure Prediction through Strategic Conformational Exploration with HelixFold-S1
Lihang Liu, Yang Liu, Xianbin Ye +6
Generating large ensembles of candidate conformations is standard for improving biomolecular structure prediction. Yet aimless sampling is inefficient and costly, producing many re…
HelixVS: Deep Learning-Enhanced Structure-Based Platform for Screening and Design
Shanzhuo Zhang, Xianbin Ye, Donglong He +3
Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible…
HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3
Jie Gao, Jing Hu, Shanzhuo Zhang +5
Antibody engineering is essential for developing therapeutics and advancing biomedical research. Traditional discovery methods often rely on time-consuming and resource-intensive e…
HelixDesign-Binder: A Scalable Production-Grade Platform for Binder Design Built on HelixFold3
Jie Gao, Jun Li, Jing Hu +5
Protein binder design is central to therapeutics, diagnostics, and synthetic biology, yet practical deployment remains challenging due to fragmented workflows, high computational c…