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• affiliation:Central South University, School of Pharmaceutical Sciences, Changsha, China
• affiliation:Hong Kong Baptist University, School of Chinese Medicine, Hong Kong

• Dongsheng Cao0002 — Anhui Medical University, Second Affiliated Hospital, Hefei, China

• 2025
• 
  [j94]
  Jing-Jie Peng,Yi-Yue Zhang,Rui-Feng Li,Wen-Jun Zhu,Hong-Rui Liu,Hui-Yin Li,Bin Liu,Dong-Sheng Cao,Jun Peng,Xiu-Ju Luo:
  Hybrid approach for drug-target interaction predictions in ischemic stroke models.Artif. Intell. Medicine161:103067 (2025)
• 
  [j93]
  Lijun Cai,Guanyu Yue,Yifan Chen,Li Wang,Xiaojun Yao,Quan Zou,Xiangzheng Fu,Dong-Sheng Cao:
  ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction.Briefings Bioinform.26(1) (2025)
• 
  [j92]
  Li Peng,Huaping Li,Sisi Yuan,Tao Meng,Yifan Chen,Xiangzheng Fu,Dongsheng Cao:
  metaCDA: A Novel Framework for CircRNA-Driven Drug Discovery Utilizing Adaptive Aggregation and Meta-Knowledge Learning.J. Chem. Inf. Model.65(4):2129-2144 (2025)
• 
  [j91]
  Lin Feng,Xiangzheng Fu,Zhenya Du,Yuting Guo,Linlin Zhuo,Yan Yang,Dong-Sheng Cao,Xiaojun Yao:
  MultiCTox: Empowering Accurate Cardiotoxicity Prediction through Adaptive Multimodal Learning.J. Chem. Inf. Model.65(7):3517-3528 (2025)
• 
  [j90]
  Jian-Wang Liu,Ke-Yi Liu,You-Chao Deng,Shao-Hua Shi,Xiang-Zheng Fu,Yue-Ping Jiang,Jing Fang,Qing Zhang,Dejun Jiang,Shao Liu,Dong-Sheng Cao:
  Uncertainty-Aware Deep Learning and Structural Feature Analysis for Reliable Nephrotoxicity Prediction.J. Chem. Inf. Model.65(17):9082-9096 (2025)
• 
  [j89]
  Kun Yang,Yifan Chen,Yanshi Wei,Mingrong Xiang,Linlin Zhuo,Xiangzheng Fu,Dong-Sheng Cao,Wenqian Zhang:
  MicroEnvPPI: Microenvironment-Aware Optimization Enables Generalizable Protein-Protein Interaction Prediction.J. Chem. Inf. Model.65(21):11860-11877 (2025)
• 
  [j88]
  Xinyu Zhang,Hao Wang,Zhenya Du,Linlin Zhuo,Xiangzheng Fu,Dongsheng Cao,Boqia Xie,Keqin Li:
  CardiOT: Towards Interpretable Drug Cardiotoxicity Prediction Using Optimal Transport and Kolmogorov-Arnold Networks.IEEE J. Biomed. Health Informatics29(3):1759-1770 (2025)
• 
  [i5]
  Shuting Jin,Yi Jiang,Yimin Liu,Tengfei Ma,Dong-Sheng Cao,Leyi Wei,Xiangrong Liu,Xiangxiang Zeng:
  DeepDR: an integrated deep-learning model web server for drug repositioning.CoRRabs/2511.08921 (2025)
• 2024
• 
  [j87]
  Jiacai Yi,Ziyi Yang,Wen-Tao Zhao,Zhi-Jiang Yang,Xiao-Chen Zhang,Chengkun Wu,Ai-Ping Lu,Dong-Sheng Cao:
  ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization.Briefings Bioinform.25(2) (2024)
• 
  [j86]
  Linlin Hou,Hongxin Xiang,Xiangxiang Zeng,Dongsheng Cao,Li Zeng,Bosheng Song:
  Attribute-guided prototype network for few-shot molecular property prediction.Briefings Bioinform.25(5) (2024)
• 
  [j85]
  Jinfu Peng,Jiacai Yi,Guoping Yang,Zhijun Huang,Dong-Sheng Cao:
  ISTransbase: an online database for inhibitor and substrate of drug transporters.Database J. Biol. Databases Curation2024 (2024)
• 
  [j84]
  Teng Liu,Zhaoyu Fang,Xin Li,Lining Zhang,Dong-Sheng Cao,Min Li,Mingzhu Yin:
  Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep.Bioinform.40(1) (2024)
• 
  [j83]
  Yun Kuang,Dongsheng Cao,Yonghui Zuo,Jinghan Yuan,Feng Lu,Yi Zou,Hong Wang,Dan Jiang,Qi Pei,Guoping Yang:
  CPhaMAS: An online platform for pharmacokinetic data analysis based on optimized parameter fitting algorithm.Comput. Methods Programs Biomed.248:108137 (2024)
• 
  [j82]
  Mingquan Liu,Chunyan Li,Ruizhe Chen,Dongsheng Cao,Xiangxiang Zeng:
  Geometric deep learning for drug discovery.Expert Syst. Appl.240:122498 (2024)
• 
  [j81]
  Yuansheng Liu,Zhenran Zhou,Xiaofeng Cao,Dongsheng Cao,Xiangxiang Zeng:
  Effective drug-target affinity prediction via generative active learning.Inf. Sci.679:121135 (2024)
• 
  [j80]
  Ning-Ning Wang,Bei Zhu,Xin-Liang Li,Shao Liu,Jian-Yu Shi,Dong-Sheng Cao:
  Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities.J. Chem. Inf. Model.64(1):96-109 (2024)
• 
  [j79]
  Jianing Fan,Shao-Hua Shi,Hong Xiang,Li Fu,Yanjing Duan,Dong-Sheng Cao,Hongwei Lu:
  Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods.J. Chem. Inf. Model.64(8):3080-3092 (2024)
• 
  [j78]
  Teng-Zhi Long,Dejun Jiang,Shao-Hua Shi,You-Chao Deng,Wenxuan Wang,Dong-Sheng Cao:
  Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence.J. Chem. Inf. Model.64(8):3222-3236 (2024)
• 
  [j77]
  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:
  DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.J. Chem. Inf. Model.64(14):5381-5391 (2024)
• 
  [j76]
  Jinfu Peng,Li Fu,Guoping Yang,Dongsheng Cao:
  Advanced AI-Driven Prediction of Pregnancy-Related Adverse Drug Reactions.J. Chem. Inf. Model.64(24):9286-9298 (2024)
• 
  [j75]
  Zhenxing Wu,Odin Zhang,Xiaorui Wang,Li Fu,Huifeng Zhao,Jike Wang,Hongyan Du,Dejun Jiang,Yafeng Deng,Dong-Sheng Cao,Chang-Yu Hsieh,Tingjun Hou:
  Leveraging language model for advanced multiproperty molecular optimization via prompt engineering.Nat. Mac. Intell.6(11):1359-1369 (2024)
• 
  [i4]
  Tengfei Ma,Xuan Lin,Tianle Li,Chaoyi Li,Long Chen,Peng Zhou,Xibao Cai,Xinyu Yang,Daojian Zeng,Dong-Sheng Cao,Xiangxiang Zeng:
  Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development.CoRRabs/2410.11550 (2024)
• 2023
• 
  [j74]
  Lei Wang,Shao-Hua Shi,Hui Li,Xiangxiang Zeng,Su-You Liu,Zhao-Qian Liu,Yafeng Deng,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Reducing false positive rate of docking-based virtual screening by active learning.Briefings Bioinform.24(1) (2023)
• 
  [j73]
  Kai-Yue Ji,Chong Liu,Zhao-Qian Liu,Yafeng Deng,Tingjun Hou,Dong-Sheng Cao:
  Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?Briefings Bioinform.24(2) (2023)
• 
  [j72]
  Teng Liu,Zhao-Yu Fang,Xin Li,Li-Ning Zhang,Dong-Sheng Cao,Mingzhu Yin:
  Graph deep learning enabled spatial domains identification for spatial transcriptomics.Briefings Bioinform.24(3) (2023)
• 
  [j71]
  Ze-Ying Feng,Xue-Hong Wu,Jun-Long Ma,Min Li,Ge-Fei He,Dong-Sheng Cao,Guo-Ping Yang:
  DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications.Briefings Bioinform.24(4) (2023)
• 
  [j70]
  Xuan Lin,Lichang Dai,Yafang Zhou,Zu-Guo Yu,Wen Zhang,Jian-Yu Shi,Dong-Sheng Cao,Li Zeng,Haowen Chen,Bosheng Song,Philip S. Yu,Xiangxiang Zeng:
  Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.Briefings Bioinform.24(4) (2023)
• 
  [j69]
  Yangyang Chen,Zixu Wang,Lei Wang,Jianmin Wang,Pengyong Li,Dongsheng Cao,Xiangxiang Zeng,Xiucai Ye,Tetsuya Sakurai:
  Deep generative model for drug design from protein target sequence.J. Cheminformatics15(1):38 (2023)
• 
  [j68]
  Su-Qing Yang,Liu-Xia Zhang,You-Jin Ge,Jin-Wei Zhang,Jian-Xin Hu,Cheng-Ying Shen,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.J. Cheminformatics15(1):48 (2023)
• 
  [j67]
  Teng-Zhi Long,Shao-Hua Shi,Shao Liu,Ai-Ping Lu,Zhao-Qian Liu,Min Li,Tingjun Hou,Dong-Sheng Cao:
  Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches.J. Chem. Inf. Model.63(1):111-125 (2023)
• 
  [j66]
  Yanqing Duan,Li Fu,Xiao-Chen Zhang,Teng-Zhi Long,Yuan-Hang He,Zhao-Qian Liu,Ai-Ping Lu,Yafeng Deng,Chang-Yu Hsieh,Tingjun Hou,Dong-Sheng Cao:
  Improved GNNs for Log D_7.4 Prediction by Transferring Knowledge from Low-Fidelity Data.J. Chem. Inf. Model.63(8):2345-2359 (2023)
• 
  [j65]
  Jike Wang,Yundian Zeng,Huiyong Sun,Junmei Wang,Xiaorui Wang,Ruofan Jin,Mingyang Wang,Xujun Zhang,Dong-Sheng Cao,Xi Chen,Chang-Yu Hsieh,Tingjun Hou:
  Molecular Generation with Reduced Labeling through Constraint Architecture.J. Chem. Inf. Model.63(11):3319-3327 (2023)
• 
  [j64]
  Gaoqi Weng,Xuanyan Cai,Dong-Sheng Cao,Hongyan Du,Chao Shen,Yafeng Deng,Qiaojun He,Bo Yang,Dan Li,Tingjun Hou:
  PROTAC-DB 2.0: an updated database of PROTACs.Nucleic Acids Res.51(D1):1367-1372 (2023)
• 
  [c1]
  Xixi Yang,Li Fu,Yafeng Deng,Yuansheng Liu,Dongsheng Cao,Xiangxiang Zeng:
  GPMO: Gradient Perturbation-Based Contrastive Learning for Molecule Optimization.IJCAI2023:4940-4948
• 
  [i3]
  Xuan Lin,Lichang Dai,Yafang Zhou,Zu-Guo Yu,Wen Zhang,Jian-Yu Shi,Dong-Sheng Cao,Li Zeng,Haowen Chen,Bosheng Song,Philip S. Yu,Xiangxiang Zeng:
  Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.CoRRabs/2306.05257 (2023)
• 2022
• 
  [j63]
  Mingyang Wang,Huiyong Sun,Jike Wang,Jinping Pang,Xin Chai,Lei Xu,Honglin Li,Dongsheng Cao,Tingjun Hou:
  Comprehensive assessment of deep generative architectures for de novo drug design.Briefings Bioinform.23(1) (2022)
• 
  [j62]
  Xi Yang,Wei Wang,Jing-Lun Ma,Yan-Long Qiu,Kai Lu,Dong-Sheng Cao,Chengkun Wu:
  BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution.Briefings Bioinform.23(1) (2022)
• 
  [j61]
  Dejun Jiang,Huiyong Sun,Jike Wang,Chang-Yu Hsieh,Yuquan Li,Zhenxing Wu,Dong-Sheng Cao,Jian Wu,Tingjun Hou:
  Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning.Briefings Bioinform.23(2) (2022)
• 
  [j60]
  Xiao-Chen Zhang,Jiacai Yi,Guo-Ping Yang,Chengkun Wu,Tingjun Hou,Dong-Sheng Cao:
  ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images.Briefings Bioinform.23(2) (2022)
• 
  [j59]
  Zhenxing Wu,Dejun Jiang,Jike Wang,Xujun Zhang,Hongyan Du,Lurong Pan,Chang-Yu Hsieh,Dongsheng Cao,Tingjun Hou:
  Knowledge-based BERT: a method to extract molecular features like computational chemists.Briefings Bioinform.23(3) (2022)
• 
  [j58]
  Zhe Wang,Hong Pan,Huiyong Sun,Yu Kang,Huanxiang Liu,Dongsheng Cao,Tingjun Hou:
  fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.Briefings Bioinform.23(5) (2022)
• 
  [j57]
  Jiacai Yi,Chengkun Wu,Xiao-Chen Zhang,Xinyi Xiao,Yanlong Qiu,Wentao Zhao,Tingjun Hou,Dong-Sheng Cao:
  MICER: a pre-trained encoder-decoder architecture for molecular image captioning.Bioinform.38(19):4562-4572 (2022)
• 
  [j56]
  Ning-Ning Wang,Xiang-Gui Wang,Guo-Li Xiong,Ziyi Yang,Ai-Ping Lu,Xiang Chen,Shao Liu,Tingjun Hou,Dong-Sheng Cao:
  Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes.J. Cheminformatics14(1):23 (2022)
• 
  [j55]
  Gaoang Wang,Jiahui Yu,Hongyan Du,Chao Shen,Xujun Zhang,Yifei Liu,Yangyang Zhang,Dong-Sheng Cao,Peichen Pan,Tingjun Hou:
  VGSC-DB: an online database of voltage-gated sodium channels.J. Cheminformatics14(1):75 (2022)
• 
  [j54]
  Liu-Xia Zhang,Jie Dong,Hui Wei,Shao-Hua Shi,Ai-Ping Lu,Gui-Ming Deng,Dong-Sheng Cao:
  TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine.J. Cheminformatics14(1):89 (2022)
• 
  [j53]
  Jiahui Yu,Jike Wang,Hong Zhao,Junbo Gao,Yu Kang,Dong-Sheng Cao,Zhe Wang,Tingjun Hou:
  Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism.J. Chem. Inf. Model.62(12):2973-2986 (2022)
• 
  [j52]
  Jialu Wu,Junmei Wang,Zhenxing Wu,Shengyu Zhang,Yafeng Deng,Yu Kang,Dong-Sheng Cao,Chang-Yu Hsieh,Tingjun Hou:
  ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction.J. Chem. Inf. Model.62(23):5975-5987 (2022)
• 
  [j51]
  Guo-Li Xiong,Zhi-Jiang Yang,Jiacai Yi,Ningning Wang,Lei Wang,Huimin Zhu,Chengkun Wu,Ai-Ping Lu,Xiang Chen,Shao Liu,Tingjun Hou,Dongsheng Cao:
  DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety.Nucleic Acids Res.50(D1):1200-1207 (2022)
• 
  [i2]
  Xiaoqin Pan,Xuan Lin,Dongsheng Cao,Xiangxiang Zeng,Philip S. Yu,Lifang He,Ruth Nussinov,Feixiong Cheng:
  Deep learning for drug repurposing: methods, databases, and applications.CoRRabs/2202.05145 (2022)
• 2021
• 
  [j50]
  Jie Dong,Min-Feng Zhu,Yong-Huan Yun,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study.Briefings Bioinform.22(1):474-484 (2021)
• 
  [j49]
  Chao Shen,Ye Hu,Zhe Wang,Xujun Zhang,Haiyang Zhong,Gaoang Wang,Xiaojun Yao,Lei Xu,Dong-Sheng Cao,Tingjun Hou:
  Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.Briefings Bioinform.22(1):497-514 (2021)
• 
  [j48]
  Chao Shen,Ye Hu,Zhe Wang,Xujun Zhang,Jinping Pang,Gaoang Wang,Haiyang Zhong,Lei Xu,Dong-Sheng Cao,Tingjun Hou:
  Beware of the generic machine learning-based scoring functions in structure-based virtual screening.Briefings Bioinform.22(3) (2021)
• 
  [j47]
  Jike Wang,Dong-Sheng Cao,Cunchen Tang,Lei Xu,Qiaojun He,Bo Yang,Xi Chen,Huiyong Sun,Tingjun Hou:
  DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.Briefings Bioinform.22(3) (2021)
• 
  [j46]
  Guo-Li Xiong,Wenling Ye,Chao Shen,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Improving structure-based virtual screening performance via learning from scoring function components.Briefings Bioinform.22(3) (2021)
• 
  [j45]
  Ziyi Yang,Zhi-Jiang Yang,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Scopy: an integrated negative design python library for desirable HTS/VS database design.Briefings Bioinform.22(3) (2021)
• 
  [j44]
  Zhenxing Wu,Minfeng Zhu,Yu Kang,Elaine Lai-Han Leung,Tailong Lei,Chao Shen,Dejun Jiang,Zhe Wang,Dong-Sheng Cao,Tingjun Hou:
  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.22(4) (2021)
• 
  [j43]
  Ziyi Yang,Jie Dong,Zhi-Jiang Yang,Mingzhu Yin,Hong-Li Jiang,Ai-Ping Lu,Xiang Chen,Tingjun Hou,Dong-Sheng Cao:
  ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds.Briefings Bioinform.22(4) (2021)
• 
  [j42]
  Li Fu,Ziyi Yang,Zhi-Jiang Yang,Mingzhu Yin,Ai-Ping Lu,Xiang Chen,Shao Liu,Tingjun Hou,Dong-Sheng Cao:
  QSAR-assisted-MMPA to expand chemical transformation space for lead optimization.Briefings Bioinform.22(5) (2021)
• 
  [j41]
  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:
  Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?Briefings Bioinform.22(5) (2021)
• 
  [j40]
  Zhenxing Wu,Dejun Jiang,Chang-Yu Hsieh,Guangyong Chen,Ben Liao,Dong-Sheng Cao,Tingjun Hou:
  Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method.Briefings Bioinform.22(5) (2021)
• 
  [j39]
  Ziyi Yang,Zhi-Jiang Yang,Yue Zhao,Mingzhu Yin,Ai-Ping Lu,Xiang Chen,Shao Liu,Tingjun Hou,Dong-Sheng Cao:
  PySmash: Python package and individual executable program for representative substructure generation and application.Briefings Bioinform.22(5) (2021)
• 
  [j38]
  Qing Ye,Xin Chai,Dejun Jiang,Liu Yang,Chao Shen,Xujun Zhang,Dan Li,Dong-Sheng Cao,Tingjun Hou:
  Identification of active molecules against Mycobacterium tuberculosis through machine learning.Briefings Bioinform.22(5) (2021)
• 
  [j37]
  Chengkun Wu,Xiao-Chen Zhang,Zhi-Jiang Yang,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules.Briefings Bioinform.22(6) (2021)
• 
  [j36]
  Xiao-Chen Zhang,Chengkun Wu,Zhi-Jiang Yang,Zhen-Xing Wu,Jiacai Yi,Chang-Yu Hsieh,Tingjun Hou,Dong-Sheng Cao:
  MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction.Briefings Bioinform.22(6) (2021)
• 
  [j35]
  Yue Zhao,Xiang-Gui Wang,Zhong-Ye Ma,Guo-Li Xiong,Zhi-Jiang Yang,Yan Cheng,Ai-Ping Lu,Zhi-Jun Huang,Dong-Sheng Cao:
  Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors.Briefings Bioinform.22(6) (2021)
• 
  [j34]
  Jike Wang,Huiyong Sun,Jiawen Chen,Dejun Jiang,Zhe Wang,Zhenxing Wu,Xi Chen,Dong-Sheng Cao,Tingjun Hou:
  DeepChargePredictor: a web server for predicting QM-based atomic charges viastate-of-the-art machine-learning algorithms.Bioinform.37(22):4255-4257 (2021)
• 
  [j33]
  Xujun Zhang,Chao Shen,Xueying Guo,Zhe Wang,Gaoqi Weng,Qing Ye,Gaoang Wang,Qiaojun He,Bo Yang,Dong-Sheng Cao,Tingjun Hou:
  ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions.J. Cheminformatics13(1):6 (2021)
• 
  [j32]
  Dejun Jiang,Zhenxing Wu,Chang-Yu Hsieh,Guangyong Chen,Ben Liao,Zhe Wang,Chao Shen,Dong-Sheng Cao,Jian Wu,Tingjun Hou:
  Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models.J. Cheminformatics13(1):12 (2021)
• 
  [j31]
  Chao Shen,Xueping Hu,Junbo Gao,Xujun Zhang,Haiyang Zhong,Zhe Wang,Lei Xu,Yu Kang,Dong-Sheng Cao,Tingjun Hou:
  The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.J. Cheminformatics13(1):81 (2021)
• 
  [j30]
  Ziyi Yang,Li Fu,Ai-Ping Lu,Shao Liu,Tingjun Hou,Dong-Sheng Cao:
  Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion.J. Cheminformatics13(1):86 (2021)
• 
  [j29]
  Hongyan Du,Junbo Gao,Gaoqi Weng,Jun-Jie Ding,Xin Chai,Jinping Pang,Yu Kang,Dan Li,Dong-Sheng Cao,Tingjun Hou:
  CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors.Nucleic Acids Res.49(Database-Issue):D1122-D1129 (2021)
• 
  [j28]
  Gaoqi Weng,Chao Shen,Dong-Sheng Cao,Junbo Gao,Xiaowu Dong,Qiaojun He,Bo Yang,Dan Li,Jian Wu,Tingjun Hou:
  PROTAC-DB: an online database of PROTACs.Nucleic Acids Res.49(Database-Issue):D1381-D1387 (2021)
• 
  [j27]
  Guo-Li Xiong,Zhenxing Wu,Jiacai Yi,Li Fu,Zhi-Jiang Yang,Chang-Yu Hsieh,Mingzhu Yin,Xiangxiang Zeng,Chengkun Wu,Aiping Lu,Xiang Chen,Tingjun Hou,Dong-Sheng Cao:
  ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties.Nucleic Acids Res.49(Webserver-Issue):5-14 (2021)
• 
  [j26]
  Jike Wang,Chang-Yu Hsieh,Mingyang Wang,Xiaorui Wang,Zhenxing Wu,Dejun Jiang,Benben Liao,Xujun Zhang,Bo Yang,Qiaojun He,Dongsheng Cao,Xi Chen,Tingjun Hou:
  Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning.Nat. Mach. Intell.3(10):914-922 (2021)
• 2020
• 
  [j25]
  Jike Wang,Dong-Sheng Cao,Cunchen Tang,Xi Chen,Huiyong Sun,Tingjun Hou:
  Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning.Bioinform.36(18):4721-4728 (2020)
• 
  [j24]
  Dejun Jiang,Tailong Lei,Zhe Wang,Chao Shen,Dong-Sheng Cao,Tingjun Hou:
  ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning.J. Cheminformatics12(1):16 (2020)
• 
  [j23]
  Li Fu,Lu Liu,Zhi-Jiang Yang,Pan Li,Jun-Jie Ding,Yong-Huan Yun,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis.J. Chem. Inf. Model.60(1):63-76 (2020)
• 
  [j22]
  Ziyi Yang,Jie Dong,Zhi-Jiang Yang,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays.J. Chem. Inf. Model.60(4):2031-2043 (2020)
• 
  [j21]
  Wenling Ye,Chao Shen,Guo-Li Xiong,Jun-Jie Ding,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.J. Chem. Inf. Model.60(9):4216-4230 (2020)

• 2019
• 
  [j20]
  Ziyi Yang,Zhi-Jiang Yang,Jie Dong,Liang-Liang Wang,Liu-Xia Zhang,Jun-Jie Ding,Xiao-Qin Ding,Ai-Ping Lu,Tingjun Hou,Dong-Sheng Cao:
  Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery.J. Chem. Inf. Model.59(9):3714-3726 (2019)
• 
  [j19]
  Zhenxing Wu,Tailong Lei,Chao Shen,Zhe Wang,Dong-Sheng Cao,Tingjun Hou:
  ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches.J. Chem. Inf. Model.59(11):4587-4601 (2019)
• 2018
• 
  [j18]
  Zhi-Zhong Liu,Jia-Wei Huang,Yong Wang,Dong-Sheng Cao:
  ECoFFeS: A Software Using Evolutionary Computation for Feature Selection in Drug Discovery.IEEE Access6:20950-20963 (2018)
• 
  [j17]
  Jie Dong,Zhi-Jiang Yao,Lin Zhang,Feijun Luo,Qinlu Lin,Ai-Ping Lu,Alex F. Chen,Dong-Sheng Cao:
  PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.J. Cheminformatics10(1):16:1-16:11 (2018)
• 
  [j16]
  Jie Dong,Ning-Ning Wang,Zhi-Jiang Yao,Lin Zhang,Yan Cheng,Defang Ouyang,Ai-Ping Lu,Dong-Sheng Cao:
  ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database.J. Cheminformatics10(1):29:1-29:11 (2018)
• 
  [j15]
  Ning-Ning Wang,Jie Dong,Lin Zhang,Defang Ouyang,Yan Cheng,Alex F. Chen,Ai-Ping Lu,Dong-Sheng Cao:
  HAMdb: a database of human autophagy modulators with specific pathway and disease information.J. Cheminformatics10(1):34:1-34:8 (2018)
• 
  [i1]
  Zhuyifan Ye,Yilong Yang,Xiaoshan Li,Dong-Sheng Cao,Defang Ouyang:
  An Integrated Transfer Learning and Multitask Learning Approach for Pharmacokinetic Parameter Prediction.CoRRabs/1812.09073 (2018)
• 2017
• 
  [j14]
  Jie Dong,Zhi-Jiang Yao,Min-Feng Zhu,Ning-Ning Wang,Ben Lu,Alex F. Chen,Ai-Ping Lu,Hongyu Miao,Wen-Bin Zeng,Dong-Sheng Cao:
  ChemSAR: an online pipelining platform for molecular SAR modeling.J. Cheminformatics9(1):27:1-27:13 (2017)
• 2016
• 
  [j13]
  Zhi-Jiang Yao,Jie Dong,Yu-Jing Che,Min-Feng Zhu,Ming Wen,Ning-Ning Wang,Shan Wang,Ai-Ping Lu,Dong-Sheng Cao:
  TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models.J. Comput. Aided Mol. Des.30(5):413-424 (2016)
• 
  [j12]
  Jie Dong,Zhi-Jiang Yao,Ming Wen,Min-Feng Zhu,Ning-Ning Wang,Hongyu Miao,Ai-Ping Lu,Wen-Bin Zeng,Dong-Sheng Cao:
  BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.J. Cheminformatics8(1):34:1-34:13 (2016)
• 
  [j11]
  Ning-Ning Wang,Jie Dong,Yin-Hua Deng,Min-Feng Zhu,Ming Wen,Zhiqiang Yao,Ai-Ping Lu,Jian-Bing Wang,Dong-Sheng Cao:
  ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting.J. Chem. Inf. Model.56(4):763-773 (2016)
• 2015
• 
  [j10]
  Dong-Sheng Cao,Nan Xiao,Qing-Song Xu,Alex F. Chen:
  Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.Bioinform.31(2):279-281 (2015)
• 
  [j9]
  Nan Xiao,Dong-Sheng Cao,Min-Feng Zhu,Qing-Song Xu:
  protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.Bioinform.31(11):1857-1859 (2015)
• 
  [j8]
  Jie Dong,Dong-Sheng Cao,Hongyu Miao,Shao Liu,Bai-Chuan Deng,Yong-Huan Yun,Ning-Ning Wang,Ai-Ping Lu,Wen-Bin Zeng,Alex F. Chen:
  ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation.J. Cheminformatics7:60:1-60:10 (2015)
• 2013
• 
  [j7]
  Dong-Sheng Cao,Qing-Song Xu,Yi-Zeng Liang:
  propy: a tool to generate various modes of Chou's PseAAC.Bioinform.29(7):960-962 (2013)
• 
  [j6]
  Dong-Sheng Cao,Qing-Song Xu,Qian-Nan Hu,Yi-Zeng Liang:
  ChemoPy: freely available python package for computational biology and chemoinformatics.Bioinform.29(8):1092-1094 (2013)
• 
  [j5]
  Dong-Sheng Cao,Yi-Zeng Liang,Jun Yan,Gui-Shan Tan,Qing-Song Xu,Shao Liu:
  PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies.J. Chem. Inf. Model.53(11):3086-3096 (2013)
• 2011
• 
  [j4]
  Qian-Nan Hu,Zhe Deng,Huanan Hu,Dong-Sheng Cao,Yi-Zeng Liang:
  RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.Bioinform.27(17):2465-2467 (2011)
• 
  [j3]
  Dongsheng Cao,Yizeng Liang,Qingsong Xu,Yifeng Yun,Hongdong Li:
  Toward better QSAR/QSPR modeling: simultaneous outlier detection and variable selection using distribution of model features.J. Comput. Aided Mol. Des.25(1):67-80 (2011)
• 
  [j2]
  Hong-Dong Li,Yi-Zeng Liang,Qing-Song Xu,Dong-Sheng Cao,Bin-Bin Tan,Bai-Chuan Deng,Chen-Chen Lin:
  Recipe for Uncovering Predictive Genes Using Support Vector Machines Based on Model Population Analysis.IEEE ACM Trans. Comput. Biol. Bioinform.8(6):1633-1641 (2011)
• 2010
• 
  [j1]
  Dong-Sheng Cao,Yi-Zeng Liang,Qing-Song Xu,Hong-Dong Li,Xian Chen:
  A new strategy of outlier detection for QSAR/QSPR.J. Comput. Chem.31(3):592-602 (2010)

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