Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches. - Peichen Pan; Youyong Li; Huidong Yu; Huiyong Sun; Tingjun Hou (J. Chem. Inf. Model., 2013)

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)

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)

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape. - Huiyong Sun; Youyong Li; Sheng Tian; Junmei Wang; Tingjun Hou (PLoS Comput. Biol., 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)

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)

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)

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)

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. - Ercheng Wang; Hui Liu; Junmei Wang; Gaoqi Weng; Huiyong Sun; Zhe Wang 041; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2020)

Causality Extraction in Futures Domain. - Yuxiang Jia; Le Kang; Huiyong Sun; Xiaojing Du; Shuai Cao; Hongying Zan; Fang Li (IALP, 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)

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. - Ercheng Wang; Weitao Fu; Dejun Jiang 002; Huiyong Sun; Junmei Wang; Xujun Zhang; Gaoqi Weng; Hui Liu; Peng Tao 007; Tingjun Hou (J. Chem. Inf. Model., 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)

Building a Corpus for Chinese Causality Extraction in Futures Domain. - Huiyong Sun; Yuxiang Jia; Xiaojing Du; Shuai Cao; Hongying Zan (CLSW (2), 2022)

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)

Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. - Rongfan Tang; Pengcheng Chen; Zhe Wang 041; Lingling Wang; Haiping Hao; Tingjun Hou; Huiyong Sun (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)

Exploring PI3Kγ binding preference with Eganelisib, Duvelisib, and Idelalisib via energetic, pharmacophore and dissociation pathway analyses. - Lei Jia; Lingling Wang; Yingmin Jiang; Lei Xu 035; Yanfei Cai; Yun Chen; Jian Jin; Huiyong Sun; Jingyu Zhu (Comput. Biol. Medicine, 2022)

Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses. - Yang Yu; Zhe Wang 041; Lingling Wang; Sheng Tian; Tingjun Hou; Huiyong Sun (J. Cheminformatics, 2022)

Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. - Qinghua Wang; Zhe Wang 041; Sheng Tian; Lingling Wang; Rongfan Tang; Yang Yu; Jingxuan Ge; Tingjun Hou; Haiping Hao; Huiyong Sun (J. Chem. Inf. Model., 2022)

Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis. - Lingling Wang; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Haiping Hao; Huiyong Sun (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)

Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. - Sutong Xiang; Zhe Wang 041; Rongfan Tang; Lingling Wang; Qinghua Wang; Yang Yu; Qirui Deng; Tingjun Hou; Haiping Hao; Huiyong Sun (J. Chem. Inf. Model., 2023)

RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning. - Qirui Deng; Zhe Wang 041; Sutong Xiang; Qinghua Wang; Yifei Liu; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. - Nanqi Hong; Dejun Jiang 002; Zhe Wang 041; Huiyong Sun; Hao Luo; Lingjie Bao; Mingli Song; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2024)

Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation. - Lingling Wang; Shu Li; Sutong Xiang; Huanxiang Liu; Huiyong Sun (J. Chem. Inf. Model., 2024)

Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation. - Kexin Xu; Zhe Wang 041; Sutong Xiang; Rongfan Tang; Qirui Deng; Jingxuan Ge; Zhiliang Jiang; Kaimo Yang; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors. - Kaimo Yang; Dejun Jiang 002; Qirui Deng; Sutong Xiang; Jingxuan Ge; Kexin Xu; Zhiliang Jiang; Zihao Wang; Chen Yin; Youqiao Qian; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2025)

Benchmarking AI-powered docking methods from the perspective of virtual screening. - Shukai Gu; Chao Shen 008; Xujun Zhang; Huiyong Sun; Heng Cai; Hao Luo; Huifeng Zhao; Bo Liu; Hongyan Du; Yihao Zhao; Chenggong Fu; Silong Zhai; et al. (Nat. Mac. Intell., 2025)