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)

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)

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)

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)

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)

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)

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)

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)

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)

Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. - Haiyi Chen; Rui Zhou; Jinping Pang; Yue Guo 008; Jiawen Chen; Yu Kang 002; Mojie Duan; Tingjun Hou (J. Chem. Inf. Model., 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)

Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. - Yuwei Yang; Zhenxing Wu; Xiaojun Yao; Yu Kang 002; Tingjun Hou; Chang-Yu Hsieh; Huanxiang Liu (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)

Learning on topological surface and geometric structure for 3D molecular generation. - Odin Zhang; Tianyue Wang; Gaoqi Weng; Dejun Jiang 002; Ning Wang; Xiaorui Wang; Huifeng Zhao; Jialu Wu; Ercheng Wang; Guangyong Chen; Yafeng Deng; Peichen Pan; et al. (Nat. Comput. Sci., 2023)

Efficient and accurate large library ligand docking with KarmaDock. - Xujun Zhang; Odin Zhang; Chao Shen 008; Wanglin Qu; Shicheng Chen; Hanqun Cao; Yu Kang 002; Zhe Wang 041; Ercheng Wang; Jintu Zhang; Yafeng Deng; Furui Liu; et al. (Nat. Comput. Sci., 2023)

Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. - Jintu Zhang; Haotian Zhang; Zhixin Qin; Yu Kang 002; Xin Hong; Tingjun Hou (J. Chem. Inf. Model., 2023)

Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? - Shukai Gu; Chao Shen 008; Jiahui Yu; Hong Zhao; Huanxiang Liu; Liwei Liu; Rong Sheng; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Yu Kang 002 (Briefings Bioinform., 2023)

Deep Generation Model Guided by the Docking Score for Active Molecular Design. - Yuwei Yang; Chang-Yu Hsieh; Yu Kang 002; Tingjun Hou; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2023)

On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. - Haiyi Chen; Yue Guo 008; Shengqing Ye; Jintu Zhang; Haotian Zhang; Na Liu; Rui Zhou; Tingjun Hou; Hongguang Xia; Yu Kang 002; Mojie Duan (J. Chem. Inf. Model., 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)

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. - Odin Zhang; Jintu Zhang; Jieyu Jin; Xujun Zhang; Renling Hu; Chao Shen 008; Hanqun Cao; Hongyan Du; Yu Kang 002; Yafeng Deng; Furui Liu; Guangyong Chen; et al. (Nat. Mac. Intell., 2023)

Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. - Zhe Wang 041; Haiyang Zhong; Jintu Zhang; Peichen Pan; Dong Wang; Huanxiang Liu; Xiaojun Yao; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2023)

TB-IECS: an accurate machine learning-based scoring function for virtual screening. - Xujun Zhang; Chao Shen 008; Dejun Jiang 002; Jintu Zhang; Qing Ye; Lei Xu 035; Tingjun Hou; Peichen Pan; Yu Kang 002 (J. Cheminformatics, 2023)

AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences. - Ruofan Jin; Qing Ye; Jike Wang; Zheng Cao; Dejun Jiang 002; Tianyue Wang; Yu Kang 002; Wanting Xu; Chang-Yu Hsieh; Tingjun Hou (Briefings Bioinform., 2024)

Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. - Tianyue Wang; Langcheng Wang; Xujun Zhang; Chao Shen 008; Odin Zhang; Jike Wang; Jialu Wu; Ruofan Jin; Donghao Zhou; Shicheng Chen; Liwei Liu; Xiaorui Wang; et al. (Briefings Bioinform., 2024)

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. - Odin Zhang; Yufei Huang 002; Shichen Cheng; Mengyao Yu; Xujun Zhang; Haitao Lin; Yundian Zeng; Mingyang Wang 004; Zhenxing Wu; Huifeng Zhao; Zaixi Zhang; Chenqing Hua; et al. (CoRR, 2024)

Token-Mol 1.0: Tokenized drug design with large language model. - Jike Wang; Rui Qin; Mingyang Wang 004; Meijing Fang; Yangyang Zhang; Yuchen Zhu; Qun Su; Qiaolin Gou; Chao Shen 008; Odin Zhang; Zhenxing Wu; Dejun Jiang 002; et al. (CoRR, 2024)

Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. - Shukai Gu; Yuwei Yang; Yihao Zhao; Jiayue Qiu; Xiaorui Wang; Henry Hoi Yee Tong; Liwei Liu; Xiaozhe Wan; Huanxiang Liu; Tingjun Hou; Yu Kang 002 (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)

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)

Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. - Huifeng Zhao; Dejun Jiang 002; Chao Shen 008; Jintu Zhang; Xujun Zhang; Xiaorui Wang; Dou Nie; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2024)

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)

A general model for predicting enzyme functions based on enzymatic reactions. - Wenjia Qian; Xiaorui Wang; Yu Kang 002; Peichen Pan; Tingjun Hou; Chang-Yu Hsieh (J. Cheminformatics, 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 Learning-Driven Insights into Enzyme-Substrate Interaction Discovery. - Wenjia Qian; Xiaorui Wang; Yuansheng Huang; Yu Kang 002; Peichen Pan; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2025)

PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction. - Silong Zhai; Huifeng Zhao; Jike Wang; Shaolong Lin; Tiantao Liu; Shukai Gu; Dejun Jiang 002; Huanxiang Liu; Yu Kang 002; Xiaojun Yao; Tingjun Hou (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)

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)

Graph Neural Networks in Modern AI-aided Drug Discovery. - Odin Zhang; Haitao Lin; Xujun Zhang; Xiaorui Wang; Zhenxing Wu; Qing Ye; Weibo Zhao; Jike Wang; Kejun Ying; Yu Kang 002; Chang-Yu Hsieh; Tingjun Hou (CoRR, 2025)

A Scalable and Quantum-Accurate Foundation Model for Biomolecular Force Field via Linearly Tensorized Quadrangle Attention. - Qun Su; Kai Zhu; Qiaolin Gou; Jintu Zhang; Renling Hu; Yurong Li; Yongze Wang; Hui Zhang; Ziyi You; Linlong Jiang; Yu Kang 002; Jike Wang; et al. (CoRR, 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)

Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates. - Xiaodan Yin; Xiaorui Wang; Zhenxing Wu; Qin Li; Yu Kang 002; Yafeng Deng; Pei Luo; Huanxiang Liu; Guqin Shi; Zheng Wang 027; Xiaojun Yao; Chang-Yu Hsieh; et al. (J. Cheminformatics, 2025)