A new strategy of outlier detection for QSAR/QSPR. - Dong-Sheng Cao 001; Yi-Zeng Liang; Qing-Song Xu; Hong-Dong Li; Xian Chen (J. Comput. Chem., 2010)

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity. - Qian-Nan Hu; Zhe Deng; Huanan Hu; Dong-Sheng Cao 001; Yi-Zeng Liang (Bioinform., 2011)

Toward better QSAR/QSPR modeling: simultaneous outlier detection and variable selection using distribution of model features. - Dongsheng Cao 001; Yizeng Liang; Qingsong Xu; Yifeng Yun; Hongdong Li (J. Comput. Aided Mol. Des., 2011)

Recipe for Uncovering Predictive Genes Using Support Vector Machines Based on Model Population Analysis. - Hong-Dong Li; Yi-Zeng Liang; Qing-Song Xu; Dong-Sheng Cao 001; Bin-Bin Tan; Bai-Chuan Deng; Chen-Chen Lin (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

ChemoPy: freely available python package for computational biology and chemoinformatics. - Dong-Sheng Cao 001; Qing-Song Xu; Qian-Nan Hu; Yi-Zeng Liang (Bioinform., 2013)

propy: a tool to generate various modes of Chou's PseAAC. - Dong-Sheng Cao 001; Qing-Song Xu; Yi-Zeng Liang (Bioinform., 2013)

PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies. - Dong-Sheng Cao 001; Yi-Zeng Liang; Jun Yan; Gui-Shan Tan; Qing-Song Xu; Shao Liu (J. Chem. Inf. Model., 2013)

Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. - Dong-Sheng Cao 001; Nan Xiao 002; Qing-Song Xu; Alex F. Chen (Bioinform., 2015)

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. - Nan Xiao 002; Dong-Sheng Cao 001; Min-Feng Zhu; Qing-Song Xu (Bioinform., 2015)

ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation. - Jie Dong; Dong-Sheng Cao 001; Hongyu Miao 001; Shao Liu; Bai-Chuan Deng; Yong-Huan Yun; Ning-Ning Wang; Aiping Lu; Wen-Bin Zeng; Alex F. Chen (J. Cheminformatics, 2015)

TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. - Zhi-Jiang Yao; Jie Dong; Yu-Jing Che; Min-Feng Zhu; Ming Wen 003; Ning-Ning Wang; Shan Wang; Aiping Lu; Dong-Sheng Cao 001 (J. Comput. Aided Mol. Des., 2016)

BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. - Jie Dong; Zhi-Jiang Yao; Ming Wen 003; Min-Feng Zhu; Ning-Ning Wang; Hongyu Miao 001; Aiping Lu; Wen-Bin Zeng; Dong-Sheng Cao 001 (J. Cheminformatics, 2016)

ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting. - Ning-Ning Wang; Jie Dong; Yin-Hua Deng; Min-Feng Zhu; Ming Wen 003; Zhiqiang Yao; Aiping Lu; Jian-Bing Wang; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2016)

ChemSAR: an online pipelining platform for molecular SAR modeling. - Jie Dong; Zhi-Jiang Yao; Min-Feng Zhu; Ning-Ning Wang; Ben Lu; Alex F. Chen; Aiping Lu; Hongyu Miao 001; Wen-Bin Zeng; Dong-Sheng Cao 001 (J. Cheminformatics, 2017)

ECoFFeS: A Software Using Evolutionary Computation for Feature Selection in Drug Discovery. - Zhi-Zhong Liu; Jia-Wei Huang; Yong Wang 002; Dong-Sheng Cao 001 (IEEE Access, 2018)

An Integrated Transfer Learning and Multitask Learning Approach for Pharmacokinetic Parameter Prediction. - Zhuyifan Ye; Yilong Yang 001; Xiaoshan Li; Dong-Sheng Cao 001; Defang Ouyang (CoRR, 2018)

ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. - Jie Dong; Ning-Ning Wang; Zhi-Jiang Yao; Lin Zhang; Yan Cheng; Defang Ouyang; Ai-Ping Lu; Dong-Sheng Cao 001 (J. Cheminformatics, 2018)

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions. - Jie Dong; Zhi-Jiang Yao; Lin Zhang; Feijun Luo; Qinlu Lin; Ai-Ping Lu; Alex F. Chen; Dong-Sheng Cao 001 (J. Cheminformatics, 2018)

HAMdb: a database of human autophagy modulators with specific pathway and disease information. - Ning-Ning Wang; Jie Dong; Lin Zhang; Defang Ouyang; Yan Cheng; Alex F. Chen; Ai-Ping Lu; Dong-Sheng Cao 001 (J. Cheminformatics, 2018)

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)

Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery. - 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 001 (J. Chem. Inf. Model., 2019)

Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning. - Jike Wang; Dong-Sheng Cao 001; Cunchen Tang; Xi Chen; Huiyong Sun; Tingjun Hou (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)

Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. - Li Fu; Lu Liu; Zhi-Jiang Yang; Pan Li; Jun-Jie Ding; Yong-Huan Yun; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2020)

Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. - Zi-Yi Yang; Jie Dong; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 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)

BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. - Jie Dong; Min-Feng Zhu; Yong-Huan Yun; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. - Li Fu; Zi-Yi Yang; Zhi-Jiang Yang; Mingzhu Yin; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

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)

DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges. - Jike Wang; Dong-Sheng Cao 001; Cunchen Tang; Lei Xu 035; Qiaojun He; Bo Yang 023; Xi Chen; Huiyong Sun; Tingjun Hou (Briefings Bioinform., 2021)

Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. - Zhenxing Wu; Dejun Jiang 002; Chang-Yu Hsieh; Guangyong Chen; Ben Liao; 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)

Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. - Chengkun Wu; Xiao-Chen Zhang; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (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)

ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. - Zi-Yi Yang; Jie Dong; Zhi-Jiang Yang; Mingzhu Yin; Hong-Li Jiang; Ai-Ping Lu; Xiang Chen; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Scopy: an integrated negative design python library for desirable HTS/VS database design. - Zi-Yi Yang; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

PySmash: Python package and individual executable program for representative substructure generation and application. - Zi-Yi Yang; Zhi-Jiang Yang; Yue Zhao; Mingzhu Yin; Ai-Ping Lu; Xiang Chen; Shao Liu; 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)

MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. - Xiao-Chen Zhang; Chengkun Wu; Zhi-Jiang Yang; Zhen-Xing Wu; Jiacai Yi; Chang-Yu Hsieh; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors. - 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 001 (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)

Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. - Zi-Yi Yang; Li Fu; Ai-Ping Lu; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (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)

CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. - Hongyan Du; Junbo Gao; Gaoqi Weng; Jun-Jie Ding; Xin Chai; Jinping Pang; Yu Kang 002; Dan Li 013; Dong-Sheng Cao 001; Tingjun Hou (Nucleic Acids Res., 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)

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. - Guo-Li Xiong; Zhenxing Wu; Jiacai Yi; Li Fu; Zhi-Jiang Yang; Chang-Yu Hsieh; Mingzhu Yin; Xiangxiang Zeng; Chengkun Wu; Ai-Ping Lu; Xiang Chen; Tingjun Hou; et al. (Nucleic Acids Res., 2021)

Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning. - Jike Wang; Chang-Yu Hsieh; Mingyang Wang 004; Xiaorui Wang; Zhenxing Wu; Dejun Jiang 002; Benben Liao; Xujun Zhang; Bo Yang 023; Qiaojun He; Dongsheng Cao 001; Xi Chen; et al. (Nat. Mach. Intell., 2021)

DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms. - Jike Wang; Huiyong Sun; Jiawen Chen; Dejun Jiang 002; Zhe Wang 041; Zhenxing Wu; Xi Chen; Dong-Sheng Cao 001; Tingjun Hou (Bioinform., 2021)

Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning. - Dejun Jiang 002; Huiyong Sun; Jike Wang; Chang-Yu Hsieh; Yuquan Li; Zhenxing Wu; Dong-Sheng Cao 001; Jian Wu 001; Tingjun Hou (Briefings Bioinform., 2022)

fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. - Zhe Wang 041; Hong Pan; Huiyong Sun; Yu Kang 002; Huanxiang Liu; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

Comprehensive assessment of deep generative architectures for de novo drug design. - Mingyang Wang 004; Huiyong Sun; Jike Wang; Jinping Pang; Xin Chai; Lei Xu 035; Honglin Li 003; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

Knowledge-based BERT: a method to extract molecular features like computational chemists. - Zhenxing Wu; Dejun Jiang 002; Jike Wang; Xujun Zhang; Hongyan Du; Lurong Pan; Chang-Yu Hsieh; Dongsheng Cao 001; Tingjun Hou (Briefings Bioinform., 2022)

BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution. - Xi Yang 020; Wei Wang; Jing-Lun Ma; Yan-Long Qiu; Kai Lu 001; Dong-Sheng Cao 001; Chengkun Wu (Briefings Bioinform., 2022)

ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images. - Xiao-Chen Zhang; Jiacai Yi; Guo-Ping Yang; Chengkun Wu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2022)

MICER: a pre-trained encoder-decoder architecture for molecular image captioning. - Jiacai Yi; Chengkun Wu; Xiao-Chen Zhang; Xinyi Xiao; Yanlong Qiu; Wentao Zhao; Tingjun Hou; Dong-Sheng Cao 001 (Bioinform., 2022)

Deep learning for drug repurposing: methods, databases, and applications. - Xiaoqin Pan; Xuan Lin; Dongsheng Cao 001; Xiangxiang Zeng; Philip S. Yu; Lifang He 001; Ruth Nussinov; Feixiong Cheng (CoRR, 2022)

Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes. - Ning-Ning Wang; Xiang-Gui Wang; Guo-Li Xiong; Zi-Yi Yang; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dong-Sheng Cao 001 (J. Cheminformatics, 2022)

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)

TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine. - Liu-Xia Zhang; Jie Dong; Hui Wei; Shao-Hua Shi; Ai-Ping Lu; Gui-Ming Deng; Dong-Sheng Cao 001 (J. Cheminformatics, 2022)

ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. - Jialu Wu; Junmei Wang; Zhenxing Wu; Shengyu Zhang; Yafeng Deng; Yu Kang 002; Dong-Sheng Cao 001; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2022)

Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. - Jiahui Yu; Jike Wang; Hong Zhao; Junbo Gao; Yu Kang 002; Dong-Sheng Cao 001; Zhe Wang 041; Tingjun Hou (J. Chem. Inf. Model., 2022)

DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. - 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 001 (Nucleic Acids Res., 2022)

GPMO: Gradient Perturbation-Based Contrastive Learning for Molecule Optimization. - Xixi Yang; Li Fu; Yafeng Deng; Yuansheng Liu; Dongsheng Cao 001; Xiangxiang Zeng (IJCAI, 2023)

Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. - Teng-Zhi Long; Shao-Hua Shi; Shao Liu; Ai-Ping Lu; Zhao-Qian Liu; Min Li 007; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2023)

Reducing false positive rate of docking-based virtual screening by active learning. - 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 001 (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)

Comprehensive assessment of nine target prediction web services: which should we choose for target fishing? - Kai-Yue Ji; Chong Liu; Zhao-Qian Liu; Yafeng Deng; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2023)

Improved GNNs for Log D7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. - 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 001 (J. Chem. Inf. Model., 2023)

Graph deep learning enabled spatial domains identification for spatial transcriptomics. - Teng Liu; Zhao-Yu Fang; Xin Li; Li-Ning Zhang; Dong-Sheng Cao 001; Mingzhu Yin (Briefings Bioinform., 2023)

Molecular Generation with Reduced Labeling through Constraint Architecture. - Jike Wang; Yundian Zeng; Huiyong Sun; Junmei Wang; Xiaorui Wang; Ruofan Jin; Mingyang Wang 004; Xujun Zhang; Dong-Sheng Cao 001; Xi Chen; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2023)

DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications. - Ze-Ying Feng; Xue-Hong Wu; Jun-Long Ma; Min Li 007; Ge-Fei He; Dong-Sheng Cao 001; Guo-Ping Yang (Briefings Bioinform., 2023)

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction. - Xuan Lin; Lichang Dai; Yafang Zhou; Zu-Guo Yu; Wen Zhang; Jian-Yu Shi; Dong-Sheng Cao 001; Li Zeng; Haowen Chen; Bosheng Song; Philip S. Yu; Xiangxiang Zeng (Briefings Bioinform., 2023)

Deep generative model for drug design from protein target sequence. - Yangyang Chen 006; Zixu Wang; Lei Wang; Jianmin Wang 016; Pengyong Li; Dongsheng Cao 001; Xiangxiang Zeng; Xiucai Ye; Tetsuya Sakurai (J. Cheminformatics, 2023)

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences. - 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 001 (J. Cheminformatics, 2023)

ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction. - Lijun Cai; Guanyu Yue; Yifan Chen; Li Wang 145; Xiaojun Yao; Quan Zou 001; Xiangzheng Fu; Dong-Sheng Cao 001 (Briefings Bioinform., 2024)

Attribute-guided prototype network for few-shot molecular property prediction. - Linlin Hou; Hongxin Xiang; Xiangxiang Zeng; Dongsheng Cao 001; Li Zeng; Bosheng Song (Briefings Bioinform., 2024)

ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization. - Jiacai Yi; Zi-Yi Yang; Wen-Tao Zhao; Zhi-Jiang Yang; Xiao-Chen Zhang; Chengkun Wu; Ai-Ping Lu; Dong-Sheng Cao 001 (Briefings Bioinform., 2024)

CPhaMAS: An online platform for pharmacokinetic data analysis based on optimized parameter fitting algorithm. - Yun Kuang; Dongsheng Cao 001; Yonghui Zuo; Jinghan Yuan; Feng Lu; Yi Zou; Hong Wang; Dan Jiang; Qi Pei; Guoping Yang (Comput. Methods Programs Biomed., 2024)

Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development. - Tengfei Ma 002; Xuan Lin; Tianle Li; Chaoyi Li; Long Chen; Peng Zhou 006; Xibao Cai; Xinyu Yang; Daojian Zeng; Dong-Sheng Cao 001; Xiangxiang Zeng (CoRR, 2024)

Geometric deep learning for drug discovery. - Mingquan Liu; Chunyan Li 002; Ruizhe Chen; Dongsheng Cao 001; Xiangxiang Zeng (Expert Syst. Appl., 2024)

Effective drug-target affinity prediction via generative active learning. - Yuansheng Liu; Zhenran Zhou; Xiaofeng Cao; Dongsheng Cao 001; Xiangxiang Zeng (Inf. Sci., 2024)

Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods. - Jianing Fan; Shao-Hua Shi; Hong Xiang; Li Fu; Yanjing Duan; Dong-Sheng Cao 001; Hongwei Lu (J. Chem. Inf. Model., 2024)

Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. - Teng-Zhi Long; Dejun Jiang 002; Shao-Hua Shi; You-Chao Deng; Wen-Xuan Wang; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2024)

Advanced AI-Driven Prediction of Pregnancy-Related Adverse Drug Reactions. - Jinfu Peng; Li Fu; Guoping Yang; Dongsheng Cao 001 (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)

Leveraging language model for advanced multiproperty molecular optimization via prompt engineering. - Zhenxing Wu; Odin Zhang; Xiaorui Wang; Li Fu; Huifeng Zhao; Jike Wang; Hongyan Du; Dejun Jiang 002; Yafeng Deng; Dong-Sheng Cao 001; Chang-Yu Hsieh; Tingjun Hou (Nat. Mac. Intell., 2024)

ISTransbase: an online database for inhibitor and substrate of drug transporters. - Jinfu Peng; Jiacai Yi; Guoping Yang; Zhijun Huang; Dong-Sheng Cao 001 (Database J. Biol. Databases Curation, 2024)

Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities. - Ning-Ning Wang; Bei Zhu; Xin-Liang Li; Shao Liu; Jian-Yu Shi; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2024)

Hybrid approach for drug-target interaction predictions in ischemic stroke models. - Jing-Jie Peng; Yi-Yue Zhang; Rui-Feng Li; Wen-Jun Zhu; Hong-Rui Liu; Hui-Yin Li; Bin Liu; Dong-Sheng Cao 001; Jun Peng; Xiu-Ju Luo (Artif. Intell. Medicine, 2025)

MultiCTox: Empowering Accurate Cardiotoxicity Prediction through Adaptive Multimodal Learning. - Lin Feng; Xiangzheng Fu; Zhenya Du; Yuting Guo; Linlin Zhuo; Yan Yang; Dong-Sheng Cao 001; Xiaojun Yao (J. Chem. Inf. Model., 2025)

metaCDA: A Novel Framework for CircRNA-Driven Drug Discovery Utilizing Adaptive Aggregation and Meta-Knowledge Learning. - Li Peng; Huaping Li; Sisi Yuan; Tao Meng; Yifan Chen; Xiangzheng Fu; Dongsheng Cao 001 (J. Chem. Inf. Model., 2025)

CardiOT: Towards Interpretable Drug Cardiotoxicity Prediction Using Optimal Transport and Kolmogorov-Arnold Networks. - Xinyu Zhang; Hao Wang; Zhenya Du; Linlin Zhuo; Xiangzheng Fu; Dongsheng Cao 001; Boqia Xie; Keqin Li 001 (IEEE J. Biomed. Health Informatics, 2025)