Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. - Yaozong Li; Jie Shen 006; Xianqiang Sun; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2010)

Estimation of ADME Properties with Substructure Pattern Recognition. - Jie Shen 006; Feixiong Cheng; You Xu; Weihua Li 005; Yun Tang 001 (J. Chem. Inf. Model., 2010)

Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers. - Feixiong Cheng; Yue Yu; Jie Shen 006; Lei Yang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2011)

Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds. - Feixiong Cheng; Yue Yu; Yadi Zhou; Zhonghua Shen; Wen Xiao; Guixia Liu; Weihua Li 005; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2011)

In Silico Assessment of Chemical Biodegradability. - Feixiong Cheng; Yutaka Ikenaga; Yadi Zhou; Yue Yu; Weihua Li 005; Jie Shen 006; Zheng Du; Lei Chen 019; Congying Xu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties. - Feixiong Cheng; Weihua Li 005; Yadi Zhou; Jie Shen 006; Zengrui Wu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening. - Guoping Hu; Guanglin Kuang; Wen Xiao; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. - Weihua Li 005; Jing Fu; Feixiong Cheng; Mingyue Zheng; Jian Zhang 037; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2012)

In silico Prediction of Chemical Ames Mutagenicity. - Congying Xu; Feixiong Cheng; Lei Chen 019; Zheng Du; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference. - Feixiong Cheng; Chuang Liu; Jing Jiang; Weiqiang Lu; Weihua Li 005; Guixia Liu; Wei-Xing Zhou; Jin Huang; Yun Tang 001 (PLoS Comput. Biol., 2012)

Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space. - Feixiong Cheng; Weihua Li 005; Zengrui Wu; Xichuan Wang; Chen Zhang; Jie Li; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2013)

Adverse Drug Events: Database Construction and in Silico Prediction. - Feixiong Cheng; Weihua Li 005; Xichuan Wang; Yadi Zhou; Zengrui Wu; Jie Shen 006; Yun Tang 001 (J. Chem. Inf. Model., 2013)

In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods. - Xiao Li 010; Lei Chen 019; Feixiong Cheng; Zengrui Wu; Hanping Bian; Congying Xu; Weihua Li 005; Guixia Liu; Xu Shen; Yun Tang 001 (J. Chem. Inf. Model., 2014)

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. - Zengrui Wu; Feixiong Cheng; Jie Li; Weihua Li 005; Guixia Liu; Yun Tang 001 (Briefings Bioinform., 2017)

Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery. - Hanwen Du; Junhao Li; Yingchun Cai; Hongxiao Zhang; Guixia Liu; Yun Tang 001; Weihua Li 005 (J. Chem. Inf. Model., 2017)

Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy. - Jiansong Fang; Zengrui Wu; Chuipu Cai; Qi Wang; Yun Tang 001; Feixiong Cheng (J. Chem. Inf. Model., 2017)

Multiclassification Prediction of Enzymatic Reactions for Oxidoreductases and Hydrolases Using Reaction Fingerprints and Machine Learning Methods. - Yingchun Cai; Hongbin Yang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2018)

ADMETopt: A Web Server for ADMET Optimization in Drug Design via Scaffold Hopping. - Hongbin Yang; Lixia Sun; Zhuang Wang; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2018)

admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. - Hongbin Yang; Chaofeng Lou; Lixia Sun; Jie Li; Yingchun Cai; Zhuang Wang; Weihua Li 005; Guixia Liu; Yun Tang 001 (Bioinform., 2019)

Computational Prediction of Site of Metabolism for UGT-Catalyzed Reactions. - Yingchun Cai; Hongbin Yang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2019)

Correction to "admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties". - Feixiong Cheng; Weihua Li 005; Yadi Zhou; Jie Shen 006; Zengrui Wu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2019)

In Silico Prediction of Endocrine Disrupting Chemicals Using Single-Label and Multilabel Models. - Lixia Sun; Hongbin Yang; Yingchun Cai; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2019)

Predicting Meridian in Chinese traditional medicine using machine learning approaches. - Yinyin Wang; Mohieddin Jafari; Yun Tang 001; Jing Tang 002 (PLoS Comput. Biol., 2019)

Insights into the antineoplastic mechanism of Chelidonium majus via systems pharmacology approach. - Xinzhe Xiao; Zehui Chen; Zengrui Wu; Tianduanyi Wang; Weihua Li 005; Guixia Liu; Bo Zhang; Yun Tang 001 (Quant. Biol., 2019)

Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. - Yue Chen; Junhao Li; Zengrui Wu; Guixia Liu; Honglin Li 003; Yun Tang 001; Weihua Li 005 (J. Chem. Inf. Model., 2020)

Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations. - Junhao Li; Yang Zhou 025; Yun Tang 001; Weihua Li 005; Yaoquan Tu (J. Chem. Inf. Model., 2020)

Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators. - Dan Teng; Jianhui Chen; Dongping Li; Zengrui Wu; Weihua Li 005; Yun Tang 001; Guixia Liu (J. Chem. Inf. Model., 2020)

NetInfer: A Web Server for Prediction of Targets and Therapeutic and Adverse Effects via Network-Based Inference Methods. - Zengrui Wu; Yayuan Peng; Zhuohang Yu; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2020)

Drug repositioning by prediction of drug's anatomical therapeutic chemical code via network-based inference approaches. - Yayuan Peng; Manjiong Wang; Yixiang Xu; Zengrui Wu; Jiye Wang; Chao Zhang; Guixia Liu; Weihua Li 005; Jian Li; Yun Tang 001 (Briefings Bioinform., 2021)

MetaADEDB 2.0: a comprehensive database on adverse drug events. - Zhuohang Yu; Zengrui Wu; Weihua Li 005; Guixia Liu; Yun Tang 001 (Bioinform., 2021)

Homotropic Cooperativity of Midazolam Metabolism by Cytochrome P450 3A4: Insight from Computational Studies. - Junhao Li; Yue Chen; Yun Tang 001; Weihua Li 005; Yaoquan Tu (J. Chem. Inf. Model., 2021)

Pathway-Based Drug Repurposing with DPNetinfer: A Method to Predict Drug-Pathway Associations via Network-Based Approaches. - Jiye Wang; Zengrui Wu; Yayuan Peng; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2021)

Discovery of Natural Products Targeting NQO1 via an Approach Combining Network-Based Inference and Identification of Privileged Substructures. - Zengrui Wu; Qiaohui Wang; Hongbin Yang; Jiye Wang; Weihua Li 005; Guixia Liu; Yi Yang 075; Yuzheng Zhao; Yun Tang 001 (J. Chem. Inf. Model., 2021)

SMINBR: An Integrated Network and Chemoinformatics Tool Specialized for Prediction of Two-Component Crystal Formation. - Lulu Zheng; Bin Zhu 012; Zengrui Wu; Fang Liang; Minghuang Hong; Guixia Liu; Weihua Li 005; Guobin Ren; Yun Tang 001 (J. Chem. Inf. Model., 2021)

Profiling prediction of nuclear receptor modulators with multi-task deep learning methods: toward the virtual screening. - Jiye Wang; Chaofeng Lou; Guixia Liu; Weihua Li 005; Zengrui Wu; Yun Tang 001 (Briefings Bioinform., 2022)

ADENet: a novel network-based inference method for prediction of drug adverse events. - Zhuohang Yu; Zengrui Wu; Weihua Li 005; Guixia Liu; Yun Tang 001 (Briefings Bioinform., 2022)

In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network. - Mengting Huang; Chaofeng Lou; Zengrui Wu; Weihua Li 005; Philip W. Lee; Yun Tang 001; Guixia Liu (J. Cheminformatics, 2022)

A multitask GNN-based interpretable model for discovery of selective JAK inhibitors. - Yimeng Wang; Yaxin Gu; Chaofeng Lou; Yuning Gong; Zengrui Wu; Weihua Li 005; Yun Tang 001; Guixia Liu (J. Cheminformatics, 2022)

Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking. - Dongping Li; Kexin Jiang; Dan Teng; Zengrui Wu; Weihua Li 005; Yun Tang 001; Rui Wang; Guixia Liu (J. Chem. Inf. Model., 2022)

IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method. - Chaofeng Lou; Hongbin Yang; Jiye Wang; Mengting Huang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2022)

Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators. - Dan Teng; Yang Zhou 025; Yun Tang 001; Guixia Liu; Yaoquan Tu (J. Chem. Inf. Model., 2022)

Identification of vital chemical information via visualization of graph neural networks. - Yimeng Wang; Mengting Huang; Hua Deng; Weihua Li 005; Zengrui Wu; Yun Tang 001; Guixia Liu (Briefings Bioinform., 2023)

ACP-MLC: A two-level prediction engine for identification of anticancer peptides and multi-label classification of their functional types. - Hua Deng; Meng Ding; Yimeng Wang; Weihua Li 005; Guixia Liu; Yun Tang 001 (Comput. Biol. Medicine, 2023)

Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods. - Moran Zhou; Jiamin Sun; Zhuohang Yu; Zengrui Wu; Weihua Li 005; Guixia Liu; Lei Ma; Rui Wang; Yun Tang 001 (J. Chem. Inf. Model., 2023)

Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features. - Yanjun Feng; Changda Gong; Jieyu Zhu; Guixia Liu; Yun Tang 001; Weihua Li 005 (J. Chem. Inf. Model., 2023)

Pharmaceutical Cocrystal Discovery via 3D-SMINBR: A New Network Recommendation Tool Augmented by 3D Molecular Conformations. - Lulu Zheng; Bin Zhu 012; Zengrui Wu; Mei Guo; Jinyao Chen; Minghuang Hong; Guixia Liu; Weihua Li 005; Guobin Ren; Yun Tang 001 (J. Chem. Inf. Model., 2023)

Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods. - Chaofeng Lou; Hongbin Yang; Hua Deng; Mengting Huang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Cheminformatics, 2023)

Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study. - Yinyin Wang; Yihang Sui; Jiaqi Yao; Hong Jiang; Qimeng Tian; Yun Tang 001; Yongyu Ou; Jing Tang 002; Ninghua Tan (Briefings Bioinform., 2024)

miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA. - Xiaolong Wu; Lehan Zhang; Xiaochu Tong; Yitian Wang; Zimei Zhang; Xiangtai Kong; Shengkun Ni; Xiaomin Luo; Mingyue Zheng; Yun Tang 001; Xutong Li (Briefings Bioinform., 2024)

ToxGIN: an In silico prediction model for peptide toxicity via graph isomorphism networks integrating peptide sequence and structure information. - Qiule Yu; Zhixing Zhang; Guixia Liu; Weihua Li 005; Yun Tang 001 (Briefings Bioinform., 2024)

MetaPredictor: in silico prediction of drug metabolites based on deep language models with prompt engineering. - Keyun Zhu; Mengting Huang; Yimeng Wang; Yaxin Gu; Weihua Li 005; Guixia Liu; Yun Tang 001 (Briefings Bioinform., 2024)

MedChatZH: A tuning LLM for traditional Chinese medicine consultations. - Yang Tan 001; Zhixing Zhang; Mingchen Li; Fei Pan; Hao Duan; Zijie Huang 001; Hua Deng; Zhuohang Yu; Chen Yang; Guoyang Shen; Peng Qi; Chengyuan Yue; et al. (Comput. Biol. Medicine, 2024)

Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. - Yanjun Feng; Changda Gong; Jieyu Zhu; Guixia Liu; Yun Tang 001; Weihua Li 005 (J. Chem. Inf. Model., 2024)

XGraphCDS: An explainable deep learning model for predicting drug sensitivity from gene pathways and chemical structures. - Yimeng Wang; Xinxin Yu; Yaxin Gu; Weihua Li 005; Keyun Zhu; Long Chen; Yun Tang 001; Guixia Liu (Comput. Biol. Medicine, 2024)

mtADENet: A novel interpretable method integrating multiple types of network-based inference approaches for prediction of adverse drug events. - Zhuohang Yu; Zengrui Wu; Moran Zhou; Long Chen; Weihua Li 005; Guixia Liu; Yun Tang 001 (Comput. Biol. Medicine, 2024)

Network-Based Methods and Their Applications in Drug Discovery. - Zhuohang Yu; Zengrui Wu; Ze Wang; Yimeng Wang; Moran Zhou; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2024)

DBPP-Predictor: a novel strategy for prediction of chemical drug-likeness based on property profiles. - Yaxin Gu; Yimeng Wang; Keyun Zhu; Weihua Li 005; Guixia Liu; Yun Tang 001 (J. Cheminformatics, 2024)

Cocry-pred: A Dynamic Resource Propagation Method for Cocrystal Prediction. - Wenxiang Song; Ren Peng; Hongbo Yu; Meiling Zhan; Guixia Liu; Weihua Li 005; Guobin Ren; Bin Zhu 012; Yun Tang 001 (J. Chem. Inf. Model., 2025)

Fluor-Predictor: An Interpretable Tool for Multiproperty Prediction and Retrieval of Fluorescent Dyes. - Wenxiang Song; Le Xiong; Xinmin Li; Yuyang Zhang; Binya Wang; Guixia Liu; Weihua Li 005; Youjun Yang; Yun Tang 001 (J. Chem. Inf. Model., 2025)

ERRα-Predictor: A Framework of Ensemble Models for Prediction of ERRα Binders, Antagonists, and Agonists Using Artificial Intelligence. - Le Xiong; Jiahao Xu; Hongbo Yu; Weihua Li 005; Xinmin Li; Wenxiang Song; Jingwei Zhang; Yun Tang 001; Guixia Liu (J. Chem. Inf. Model., 2025)

TCnet: A Novel Strategy to Predict Target Combination of Alzheimer's Disease via Network-Based Methods. - Chengyuan Yue; Baiyu Chen; Fei Pan; Ze Wang; Hongbo Yu; Guixia Liu; Weihua Li 005; Rui Wang; Yun Tang 001 (J. Chem. Inf. Model., 2025)