Dong-Sheng Cao

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 65

Top Topics

Scoring Functions

Top Venues

Briefings Bioinform.

J. Cheminformatics

J. Chem. Inf. Model.

Publications

Teng-Zhi Long, Dejun Jiang, Shao-Hua Shi, You-Chao Deng, Wen-Xuan Wang, Dong-Sheng Cao
Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. J. Chem. Inf. Model. 64 (8) (2024)
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) (2024)
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 Curation 2024 (2024)
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) (2024)
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) (2024)
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. CoRR (2023)
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)
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) (2023)
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
Prediction by Transferring Knowledge from Low-Fidelity Data. J. Chem. Inf. Model. 63 (8) (2023)
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) (2023)
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)
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)
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) (2023)
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. Cheminformatics 15 (1) (2023)
Teng Liu, Zhao-Yu Fang, Xin Li, Li-Ning Zhang, Dong-Sheng Cao, Ming-Zhu Yin
Graph deep learning enabled spatial domains identification for spatial transcriptomics. Briefings Bioinform. 24 (3) (2023)
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)
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)
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) (2022)
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)
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. Cheminformatics 14 (1) (2022)
Jia-Cai 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) (2022)
Xiao-Chen Zhang, Jia-Cai 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)
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. Cheminformatics 14 (1) (2022)
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) (2022)
Ning-Ning Wang, Xiang-Gui Wang, Guo-Li Xiong, Zi-Yi 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. Cheminformatics 14 (1) (2022)
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)
Zi-Yi 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. Cheminformatics 13 (1) (2021)
Jike Wang, Huiyong Sun, Jiawen Chen, Dejun Jiang, Zhe Wang, Zhenxing Wu, Xi Chen, Dong-Sheng Cao, Tingjun Hou
machine-learning algorithms. Bioinform. 37 (22) (2021)
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)
Guo-Li Xiong, Zhenxing Wu, Jia-Cai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Ai-Ping 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) (2021)
Zi-Yi Yang, Zhi-Jiang Yang, Yue Zhao, Ming-Zhu 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)
Zi-Yi 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)
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. Cheminformatics 13 (1) (2021)
Zi-Yi 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)
Li Fu, Zi-Yi Yang, Zhi-Jiang Yang, Ming-Zhu 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)
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)
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)
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)
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)
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)
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) (2021)
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) (2021)
Guo-Li Xiong, Wen-Ling 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)
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. Cheminformatics 13 (1) (2021)
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. Cheminformatics 13 (1) (2021)
Xiao-Chen Zhang, Chengkun Wu, Zhi-Jiang Yang, Zhen-Xing Wu, Jia-Cai 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)
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)
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) (2021)
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) (2021)
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) (2020)
Wen-Ling 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) (2020)
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. Cheminformatics 12 (1) (2020)
Zi-Yi 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) (2020)
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) (2020)
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) (2019)
Zi-Yi 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) (2019)
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. Cheminformatics 10 (1) (2018)
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. Cheminformatics 10 (1) (2018)
Zhuyifan Ye, Yilong Yang, Xiaoshan Li, Dong-Sheng Cao, Defang Ouyang
An Integrated Transfer Learning and Multitask Learning Approach for Pharmacokinetic Parameter Prediction. CoRR (2018)
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. Cheminformatics 10 (1) (2018)
Zhi-Zhong Liu, Jia-Wei Huang, Yong Wang, Dong-Sheng Cao
ECoFFeS: A Software Using Evolutionary Computation for Feature Selection in Drug Discovery. IEEE Access 6 (2018)
Jie Dong, Zhi-Jiang Yao, Min-Feng Zhu, Ning-Ning Wang, Ben Lu, Alex F. Chen, Aiping Lu, Hongyu Miao, Wen-Bin Zeng, Dong-Sheng Cao
ChemSAR: an online pipelining platform for molecular SAR modeling. J. Cheminformatics 9 (1) (2017)
Zhi-Jiang Yao, Jie Dong, Yu-Jing Che, Min-Feng Zhu, Ming Wen, Ning-Ning Wang, Shan Wang, Aiping 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) (2016)
Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hongyu Miao, Aiping 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. Cheminformatics 8 (1) (2016)
Ning-Ning Wang, Jie Dong, Yin-Hua Deng, Min-Feng Zhu, Ming Wen, Zhiqiang Yao, Aiping 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) (2016)
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) (2015)
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) (2015)
Jie Dong, Dong-Sheng Cao, Hongyu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Aiping Lu, Wen-Bin Zeng, Alex F. Chen
ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation. J. Cheminformatics 7 (2015)
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) (2013)
Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang
propy: a tool to generate various modes of Chou's PseAAC. Bioinform. 29 (7) (2013)
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) (2013)
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) (2011)
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) (2011)
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) (2010)