ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches. - Zhenxing Wu; Tailong Lei; Chao Shen 008; Zhe Wang 041; Dong-Sheng Cao 001; Tingjun Hou (J. Chem. Inf. Model., 2019)

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. - Chao Shen 008; Zhe Wang 041; Xiaojun Yao; Youyong Li; Tailong Lei; Ercheng Wang; Lei Xu 035; Feng Zhu 004; Dan Li 013; Tingjun Hou (Briefings Bioinform., 2020)

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. - Dejun Jiang 002; Tailong Lei; Zhe Wang 041; Chao Shen 008; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2020)

Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. - Wenling Ye; Chao Shen 008; Guo-Li Xiong; Jun-Jie Ding; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2020)

Beware of the generic machine learning-based scoring functions in structure-based virtual screening. - Chao Shen 008; Ye Hu; Zhe Wang 041; Xujun Zhang; Jinping Pang; Gaoang Wang; Haiyang Zhong; Lei Xu 035; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. - Chao Shen 008; Ye Hu; Zhe Wang 041; Xujun Zhang; Haiyang Zhong; Gaoang Wang; Xiaojun Yao; Lei Xu 035; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? - Chao Shen 008; Gaoqi Weng; Xujun Zhang; Elaine Lai-Han Leung; Xiaojun Yao; Jinping Pang; Xin Chai; Dan Li 013; Ercheng Wang; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets. - Zhenxing Wu; Minfeng Zhu; Yu Kang 002; Elaine Lai-Han Leung; Tailong Lei; Chao Shen 008; Dejun Jiang 002; Zhe Wang 041; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Improving structure-based virtual screening performance via learning from scoring function components. - Guo-Li Xiong; Wenling Ye; Chao Shen 008; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Identification of active molecules against Mycobacterium tuberculosis through machine learning. - Qing Ye; Xin Chai; Dejun Jiang 002; Liu Yang; Chao Shen 008; Xujun Zhang; Dan Li 013; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models. - Dejun Jiang 002; Zhenxing Wu; Chang-Yu Hsieh; Guangyong Chen; Ben Liao; Zhe Wang 041; Chao Shen 008; Dong-Sheng Cao 001; Jian Wu 001; Tingjun Hou (J. Cheminformatics, 2021)

The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. - Chao Shen 008; Xueping Hu; Junbo Gao; Xujun Zhang; Haiyang Zhong; Zhe Wang 041; Lei Xu 035; Yu Kang 002; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2021)

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. - Xujun Zhang; Chao Shen 008; Xueying Guo; Zhe Wang 041; Gaoqi Weng; Qing Ye; Gaoang Wang; Qiaojun He; Bo Yang 023; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2021)

PROTAC-DB: an online database of PROTACs. - Gaoqi Weng; Chao Shen 008; Dong-Sheng Cao 001; Junbo Gao; Xiaowu Dong; Qiaojun He; Bo Yang 023; Dan Li 013; Jian Wu 001; Tingjun Hou (Nucleic Acids Res., 2021)

VGSC-DB: an online database of voltage-gated sodium channels. - Gaoang Wang; Jiahui Yu; Hongyan Du; Chao Shen 008; Xujun Zhang; Yifei Liu; Yangyang Zhang; Dong-Sheng Cao 001; Peichen Pan; Tingjun Hou (J. Cheminformatics, 2022)

Efficient and accurate large library ligand docking with KarmaDock. - Xujun Zhang; Odin Zhang; Chao Shen 008; Wanglin Qu; Shicheng Chen; Hanqun Cao; Yu Kang 002; Zhe Wang 041; Ercheng Wang; Jintu Zhang; Yafeng Deng; Furui Liu; et al. (Nat. Comput. Sci., 2023)

Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors. - Dong Wang; Zhenxing Wu; Chao Shen 008; Lingjie Bao; Hao Luo; Zhe Wang 041; Hucheng Yao; De-Xin Kong; Cheng Luo; Tingjun Hou (Briefings Bioinform., 2023)

PROTAC-DB 2.0: an updated database of PROTACs. - Gaoqi Weng; Xuanyan Cai; Dong-Sheng Cao 001; Hongyan Du; Chao Shen 008; Yafeng Deng; Qiaojun He; Bo Yang 023; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2023)

Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? - Shukai Gu; Chao Shen 008; Jiahui Yu; Hong Zhao; Huanxiang Liu; Liwei Liu; Rong Sheng; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Yu Kang 002 (Briefings Bioinform., 2023)

ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. - Xujun Zhang; Chao Shen 008; Tianyue Wang; Yafeng Deng; Yu Kang 002; Dan Li 013; Tingjun Hou; Peichen Pan (Briefings Bioinform., 2023)

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. - Odin Zhang; Jintu Zhang; Jieyu Jin; Xujun Zhang; Renling Hu; Chao Shen 008; Hanqun Cao; Hongyan Du; Yu Kang 002; Yafeng Deng; Furui Liu; Guangyong Chen; et al. (Nat. Mac. Intell., 2023)

TB-IECS: an accurate machine learning-based scoring function for virtual screening. - Xujun Zhang; Chao Shen 008; Dejun Jiang 002; Jintu Zhang; Qing Ye; Lei Xu 035; Tingjun Hou; Peichen Pan; Yu Kang 002 (J. Cheminformatics, 2023)

Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. - Tianyue Wang; Langcheng Wang; Xujun Zhang; Chao Shen 008; Odin Zhang; Jike Wang; Jialu Wu; Ruofan Jin; Donghao Zhou; Shicheng Chen; Liwei Liu; Xiaorui Wang; et al. (Briefings Bioinform., 2024)

Token-Mol 1.0: Tokenized drug design with large language model. - Jike Wang; Rui Qin; Mingyang Wang 004; Meijing Fang; Yangyang Zhang; Yuchen Zhu; Qun Su; Qiaolin Gou; Chao Shen 008; Odin Zhang; Zhenxing Wu; Dejun Jiang 002; et al. (CoRR, 2024)

Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays. - He Liu; Chao Shen 008; Haonan Li; Tingjun Hou; Yongliang Yang 005 (J. Chem. Inf. Model., 2024)

DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. - Chao Shen 008; Jianfei Song; Chang-Yu Hsieh; Dong-Sheng Cao 001; Yu Kang 002; Wenling Ye; Zhenxing Wu; Jike Wang; Odin Zhang; Xujun Zhang; Hao Zeng; Heng Cai; et al. (J. Chem. Inf. Model., 2024)

Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. - Huifeng Zhao; Dejun Jiang 002; Chao Shen 008; Jintu Zhang; Xujun Zhang; Xiaorui Wang; Dou Nie; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2024)

Benchmarking AI-powered docking methods from the perspective of virtual screening. - Shukai Gu; Chao Shen 008; Xujun Zhang; Huiyong Sun; Heng Cai; Hao Luo; Huifeng Zhao; Bo Liu; Hongyan Du; Yihao Zhao; Chenggong Fu; Silong Zhai; et al. (Nat. Mac. Intell., 2025)

BioScore: A Foundational Scoring Function For Diverse Biomolecular Complexes. - Yuchen Zhu; Jihong Chen; Yitong Li; Xiaomin Fang; Xianbin Ye; Jingzhou He; Xujun Zhang; Jingxuan Ge; Chao Shen 008; Xiaonan Zhang; Tingjun Hou; Chang-Yu Hsieh (CoRR, 2025)