Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches. - Huiyong Sun; Youyong Li; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design. - Sheng Tian; Youyong Li; Dan Li 013; Xiaojie Xu; Junmei Wang; Qian Zhang 063; Tingjun Hou (J. Chem. Inf. Model., 2013)

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures. - Sheng Tian; Huiyong Sun; Youyong Li; Peichen Pan; Dan Li 013; Tingjun Hou (J. Chem. Inf. Model., 2013)

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility. - Sheng Tian; Huiyong Sun; Peichen Pan; Dan Li 013; Xuechu Zhen; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2014)

Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models. - Peichen Pan; Sheng Tian; Huiyong Sun; Xiaotian Kong; Wenfang Zhou; Dan Li 013; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2015)

Structure-Activity Relationships and Anti-inflammatory Activities of N-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors. - Yu Zhang; Lei Xu 035; Zhiqiang Zhang; Zhiyu Zhang; Longtai Zheng; Dan Li 013; Youyong Li; Feng Liu; Kunqian Yu; Tingjun Hou; Xuechu Zhen (J. Chem. Inf. Model., 2015)

ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling. - Tailong Lei; Youyong Li; Yunlong Song; Dan Li 013; Huiyong Sun; Tingjun Hou (J. Cheminformatics, 2016)

HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. - Ting Feng; Fu Chen; Yu Kang 002; Huiyong Sun; Hui Liu; Dan Li 013; Feng Zhu 004; Tingjun Hou (J. Cheminformatics, 2017)

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. - Jun Shang; Huiyong Sun; Hui Liu; Fu Chen; Sheng Tian; Peichen Pan; Dan Li 013; De-Xin Kong; Tingjun Hou (J. Cheminformatics, 2017)

Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. - Huiyong Sun; Youyong Li; Mingyun Shen; Dan Li 013; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2017)

Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays. - Wenfang Zhou; Mojie Duan; Weitao Fu; Jinping Pang; Qin Tang; Huiyong Sun; Lei Xu 035; Shan Chang; Dan Li 013; Tingjun Hou (Genom. Proteom. Bioinform., 2018)

Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator. - Na Liu; Wenfang Zhou; Yue Guo 008; Junmei Wang; Weitao Fu; Huiyong Sun; Dan Li 013; Mojie Duan; Tingjun Hou (J. Chem. Inf. Model., 2018)

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. - Jun Shang; Ben Hu; Junmei Wang; Feng Zhu 004; Yu Kang 002; Dan Li 013; Huiyong Sun; De-Xin Kong; Tingjun Hou (J. Chem. Inf. Model., 2018)

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. - Zhe Wang 041; Xuwen Wang; Youyong Li; Tailong Lei; Ercheng Wang; Dan Li 013; Yu Kang 002; Feng Zhu 004; Tingjun Hou (Bioinform., 2019)

Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. - Ye Jin; Mojie Duan; Xuwen Wang; Xiaotian Kong; Wenfang Zhou; Huiyong Sun; Hui Liu; Dan Li 013; Huidong Yu; Youyong Li; Tingjun Hou (J. Chem. Inf. Model., 2019)

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. - Gaoqi Weng; Ercheng Wang; Zhe Wang 041; Hui Liu; Feng Zhu 004; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2019)

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. - Chao Shen 008; Zhe Wang 041; Xiaojun Yao; Youyong Li; Tailong Lei; Ercheng Wang; Lei Xu 035; Feng Zhu 004; Dan Li 013; Tingjun Hou (Briefings Bioinform., 2020)

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)

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)

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)

ReMODE: a deep learning-based web server for target-specific drug design. - Mingyang Wang 004; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Honglin Li 003; Chang-Yu Hsieh; Tingjun Hou (J. Cheminformatics, 2022)

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)

ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. - Xujun Zhang; Chao Shen 008; Tianyue Wang; Yafeng Deng; Yu Kang 002; Dan Li 013; Tingjun Hou; Peichen Pan (Briefings Bioinform., 2023)

Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. - Mingyang Wang 004; Zhengjian Wu; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Xiaojun Yao; Zhitong Bing; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2024)

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. - Dou Nie; Huifeng Zhao; Odin Zhang; Gaoqi Weng; Hui Zhang; Jieyu Jin; Haitao Lin; Yufei Huang 002; Liwei Liu; Dan Li 013; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2025)

Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein. - Shicheng Chen; Odin Zhang; Chenran Jiang; Huifeng Zhao; Xujun Zhang; Mengting Chen; Yun Liu; Qun Su; Zhenxing Wu; Xinyue Wang; Wanglin Qu; Yuanyi Ye; et al. (Nat. Mac. Intell., 2025)

ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction. - Dong Wang; Jieyu Jin; Guqin Shi; Jingxiao Bao; Zheng Wang 027; Shimeng Li; Peichen Pan; Dan Li 013; Yu Kang 002; Tingjun Hou (J. Cheminformatics, 2025)