Chao Shen

29 papers Journal 29
YearRankTypeTitle / Venue / Authors
2025 J jnl
Benchmarking AI-powered docking methods from the perspective of virtual screening.
Nat. Mac. Intell.
Shukai Gu, Chao Shen, Xujun Zhang, Huiyong Sun, Heng Cai, Hao Luo, Huifeng Zhao, Bo Liu, Hongyan Du, Yihao Zhao, Chenggong Fu, Silong Zhai, Yafeng Deng, Huanxiang Liu, Tingjun Hou, Yu Kang
2025 J jnl
BioScore: A Foundational Scoring Function For Diverse Biomolecular Complexes.
CoRR
Yuchen Zhu, Jihong Chen, Yitong Li, Xiaomin Fang, Xianbin Ye, Jingzhou He, Xujun Zhang, Jingxuan Ge, Chao Shen, Xiaonan Zhang, Tingjun Hou, Chang-Yu Hsieh
2024 J jnl
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes.
J. Chem. Inf. Model.
Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
2024 J jnl
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.
Briefings Bioinform.
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Tingjun Hou
2024 J jnl
Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays.
J. Chem. Inf. Model.
He Liu, Chao Shen, Haonan Li, Tingjun Hou, Yongliang Yang
2024 J jnl
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.
J. Chem. Inf. Model.
Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou
2024 J jnl
Token-Mol 1.0: Tokenized drug design with large language model.
CoRR
Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
Briefings Bioinform.
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
2023 J jnl
Efficient and accurate large library ligand docking with KarmaDock.
Nat. Comput. Sci.
Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors.
Briefings Bioinform.
Dong Wang, Zhenxing Wu, Chao Shen, Lingjie Bao, Hao Luo, Zhe Wang, Hucheng Yao, De-Xin Kong, Cheng Luo, Tingjun Hou
2023 J jnl
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions.
Briefings Bioinform.
Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Tingjun Hou, Peichen Pan
2023 J jnl
PROTAC-DB 2.0: an updated database of PROTACs.
Nucleic Acids Res.
Gaoqi Weng, Xuanyan Cai, Dong-Sheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou
2023 J jnl
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling.
Nat. Mac. Intell.
Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
TB-IECS: an accurate machine learning-based scoring function for virtual screening.
J. Cheminformatics
Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan, Yu Kang
2022 J jnl
VGSC-DB: an online database of voltage-gated sodium channels.
J. Cheminformatics
Gaoang Wang, Jiahui Yu, Hongyan Du, Chao Shen, Xujun Zhang, Yifei Liu, Yangyang Zhang, Dong-Sheng Cao, Peichen Pan, Tingjun Hou
2021 J jnl
ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions.
J. Cheminformatics
Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?
Briefings Bioinform.
Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Beware of the generic machine learning-based scoring functions in structure-based virtual screening.
Briefings Bioinform.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.
Briefings Bioinform.
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models.
J. Cheminformatics
Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dong-Sheng Cao, Jian Wu, Tingjun Hou
2021 J jnl
Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets.
Briefings Bioinform.
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Identification of active molecules against Mycobacterium tuberculosis through machine learning.
Briefings Bioinform.
Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Improving structure-based virtual screening performance via learning from scoring function components.
Briefings Bioinform.
Guo-Li Xiong, Wenling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2021 J jnl
PROTAC-DB: an online database of PROTACs.
Nucleic Acids Res.
Gaoqi Weng, Chao Shen, Dong-Sheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou
2021 J jnl
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.
J. Cheminformatics
Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dong-Sheng Cao, Tingjun Hou
2020 J jnl
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning.
J. Cheminformatics
Dejun Jiang, Tailong Lei, Zhe Wang, Chao Shen, Dong-Sheng Cao, Tingjun Hou
2020 J jnl
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power.
Briefings Bioinform.
Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou
2020 J jnl
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.
J. Chem. Inf. Model.
Wenling Ye, Chao Shen, Guo-Li Xiong, Jun-Jie Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2019 J jnl
ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.
J. Chem. Inf. Model.
Zhenxing Wu, Tailong Lei, Chao Shen, Zhe Wang, Dong-Sheng Cao, Tingjun Hou