Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge. - Zhaofeng Ye; Matthew P. Baumgartner; Bentley M. Wingert; Carlos J. Camacho (J. Comput. Aided Mol. Des., 2016)

Predicting protein targets for drug-like compounds using transcriptomics. - Nicolas A. Pabon; Yan Xia; Samuel K. Estabrooks; Zhaofeng Ye; Amanda K. Herbrand; Evelyn Süß; Ricardo M. Biondi; Victoria A. Assimon; Jason E. Gestwicki; Jeffrey L. Brodsky; Carlos J. Camacho; Ziv Bar-Joseph (PLoS Comput. Biol., 2018)

SPLDExtraTrees: Robust machine learning approach for predicting kinase inhibitor resistance. - Ziyi Yang; Zhaofeng Ye; Yijia Xiao; Chang-Yu Hsieh (CoRR, 2021)

SPLDExtraTrees: robust machine learning approach for predicting kinase inhibitor resistance. - Zi-Yi Yang; Zhaofeng Ye; Yijia Xiao; Chang-Yu Hsieh; Sheng-Yu Zhang (Briefings Bioinform., 2022)

Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform. - Jonathan P. Mailoa; Zhaofeng Ye; Jiezhong Qiu; Chang-Yu Hsieh; Shengyu Zhang 002 (CoRR, 2023)

TensorCircuit: a Quantum Software Framework for the NISQ Era. - Shi-Xin Zhang; Jonathan Allcock; Zhou-Quan Wan; Shuo Liu; Jiace Sun; Hao Yu; Xing-Han Yang; Jiezhong Qiu; Zhaofeng Ye; Yu-Qin Chen; Chee-Kong Lee; Yicong Zheng; et al. (Quantum, 2023)

Improved the heterodimer protein complex prediction with protein language models. - Bo Chen 026; Ziwei Xie; Jiezhong Qiu; Zhaofeng Ye; Jinbo Xu; Jie Tang 001 (Briefings Bioinform., 2023)

Multi-task bioassay pre-training for protein-ligand binding affinity prediction. - Jiaxian Yan; Zhaofeng Ye; Ziyi Yang; Chengqiang Lu; Shengyu Zhang; Qi Liu; Jiezhong Qiu (Briefings Bioinform., 2023)