A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid Preference. - Zhong-Ru Xie; Ming-Jing Hwang (APBC, 2006)

An interaction-motif-based scoring function for protein-ligand docking. - Zhong-Ru Xie; Ming-Jing Hwang (BMC Bioinform., 2010)

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. - Zhong-Ru Xie; Ming-Jing Hwang (Bioinform., 2012)

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. - Zhong-Ru Xie; Chuan-Kun Liu; Fang-Chih Hsiao; Adam Yao; Ming-Jing Hwang (Nucleic Acids Res., 2013)

Decomposing the space of protein quaternary structures with the interface fragment pair library. - Zhong-Ru Xie; Jiawen Chen; Yinghao Wu (BMC Bioinform., 2015)

Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method. - Jiawen Chen; Zhong-Ru Xie; Yinghao Wu (J. Comput. Biol., 2016)

DeepFlu: a deep learning approach for forecasting symptomatic influenza A infection based on pre-exposure gene expression. - Anna Zan; Zhong-Ru Xie; Yi-Chen Hsu; Yu-Hao Chen; Tsung-Hsien Lin; Yong-Shan Chang; Kuan Y. Chang (Comput. Methods Programs Biomed., 2022)