Yu Kang

47 papers Journal 47
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Scalable and Quantum-Accurate Foundation Model for Biomolecular Force Field via Linearly Tensorized Quadrangle Attention.
CoRR
Qun Su, Kai Zhu, Qiaolin Gou, Jintu Zhang, Renling Hu, Yurong Li, Yongze Wang, Hui Zhang, Ziyi You, Linlong Jiang, Yu Kang, Jike Wang, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
ADMET evaluation in drug discovery: 21. Application and industrial validation of machine learning algorithms for Caco-2 permeability prediction.
J. Cheminformatics
Dong Wang, Jieyu Jin, Guqin Shi, Jingxiao Bao, Zheng Wang, Shimeng Li, Peichen Pan, Dan Li, Yu Kang, Tingjun Hou
2025 J jnl
Benchmarking AI-powered docking methods from the perspective of virtual screening.
Nat. Mac. Intell.
Shukai Gu, Chao Shen, Xujun Zhang, Huiyong Sun, Heng Cai, Hao Luo, Huifeng Zhao, Bo Liu, Hongyan Du, Yihao Zhao, Chenggong Fu, Silong Zhai, Yafeng Deng, Huanxiang Liu, Tingjun Hou, Yu Kang
2025 J jnl
ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction.
J. Chem. Inf. Model.
Qiaolin Gou, Qun Su, Jike Wang, Hui Zhang, Huiyong Sun, Xujun Zhang, Linlong Jiang, Meijing Fang, Yu Kang, Huanxiang Liu, Tingjun Hou, Chang-Yu Hsieh
2025 J jnl
Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery.
J. Chem. Inf. Model.
Wenjia Qian, Xiaorui Wang, Yuansheng Huang, Yu Kang, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein.
Nat. Mac. Intell.
Shicheng Chen, Odin Zhang, Chenran Jiang, Huifeng Zhao, Xujun Zhang, Mengting Chen, Yun Liu, Qun Su, Zhenxing Wu, Xinyue Wang, Wanglin Qu, Yuanyi Ye, Xin Chai, Ning Wang, Tianyue Wang, Yuan An, Guanlin Wu, Qianqian Yang, Jiean Chen, Wei Xie, Haitao Lin, Dan Li, Chang-Yu Hsieh, Yong Huang, Yu Kang, Tingjun Hou, Peichen Pan
2025 J jnl
Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation.
J. Chem. Inf. Model.
Dou Nie, Huifeng Zhao, Odin Zhang, Gaoqi Weng, Hui Zhang, Jieyu Jin, Haitao Lin, Yufei Huang, Liwei Liu, Dan Li, Tingjun Hou, Yu Kang
2025 J jnl
ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.
Nat. Comput. Sci.
Odin Zhang, Jieyu Jin, Zhenxing Wu, Jintu Zhang, Po Yuan, Yuntao Yu, Haitao Lin, Haiyang Zhong, Xujun Zhang, Chenqing Hua, Weibo Zhao, Zhengshuo Zhang, Kejun Ying, Yufei Huang, Huifeng Zhao, Yu Kang, Peichen Pan, Jike Wang, Dong Guo, Shuangjia Zheng, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
Graph Neural Networks in Modern AI-aided Drug Discovery.
CoRR
Odin Zhang, Haitao Lin, Xujun Zhang, Xiaorui Wang, Zhenxing Wu, Qing Ye, Weibo Zhao, Jike Wang, Kejun Ying, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
2025 J jnl
Improving the predictive performance of binding affinities and poses for protein-cyclic peptide complexes through fine-tuned MM/PBSA(GBSA)-based methods.
Briefings Bioinform.
Huifeng Zhao, Jianxiang Huang, Gaoqi Weng, Dejun Jiang, Renling Hu, Yu Kang, Tingjun Hou
2025 J jnl
PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction.
J. Chem. Inf. Model.
Silong Zhai, Huifeng Zhao, Jike Wang, Shaolong Lin, Tiantao Liu, Shukai Gu, Dejun Jiang, Huanxiang Liu, Yu Kang, Xiaojun Yao, Tingjun Hou
2025 J jnl
Revisiting Protein-Protein Docking: A Systematic Evaluation Framework.
J. Chem. Inf. Model.
Linlong Jiang, Ke Zhang, Kai Zhu, Ying Wang, Yu Kang, Tingjun Hou
2025 J jnl
Syn-MolOpt: a synthesis planning-driven molecular optimization method using data-derived functional reaction templates.
J. Cheminformatics
Xiaodan Yin, Xiaorui Wang, Zhenxing Wu, Qin Li, Yu Kang, Yafeng Deng, Pei Luo, Huanxiang Liu, Guqin Shi, Zheng Wang, Xiaojun Yao, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
A general model for predicting enzyme functions based on enzymatic reactions.
J. Cheminformatics
Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh
2024 J jnl
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences.
Briefings Bioinform.
Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes.
J. Chem. Inf. Model.
Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
2024 J jnl
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.
Briefings Bioinform.
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Tingjun Hou
2024 J jnl
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation.
CoRR
Odin Zhang, Yufei Huang, Shichen Cheng, Mengyao Yu, Xujun Zhang, Haitao Lin, Yundian Zeng, Mingyang Wang, Zhenxing Wu, Huifeng Zhao, Zaixi Zhang, Chenqing Hua, Yu Kang, Sunliang Cui, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.
J. Chem. Inf. Model.
Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou
2024 J jnl
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios.
J. Chem. Inf. Model.
Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang
2024 J jnl
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.
J. Chem. Inf. Model.
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
Token-Mol 1.0: Tokenized drug design with large language model.
CoRR
Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
2024 J jnl
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides.
J. Chem. Inf. Model.
Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou
2023 J jnl
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
Briefings Bioinform.
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
2023 J jnl
Deep Generation Model Guided by the Docking Score for Active Molecular Design.
J. Chem. Inf. Model.
Yuwei Yang, Chang-Yu Hsieh, Yu Kang, Tingjun Hou, Huanxiang Liu, Xiaojun Yao
2023 J jnl
Efficient and accurate large library ligand docking with KarmaDock.
Nat. Comput. Sci.
Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
Learning on topological surface and geometric structure for 3D molecular generation.
Nat. Comput. Sci.
Odin Zhang, Tianyue Wang, Gaoqi Weng, Dejun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions.
Briefings Bioinform.
Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Tingjun Hou, Peichen Pan
2023 J jnl
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate.
J. Chem. Inf. Model.
Haiyi Chen, Yue Guo, Shengqing Ye, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou, Hongguang Xia, Yu Kang, Mojie Duan
2023 J jnl
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials.
J. Chem. Inf. Model.
Jintu Zhang, Haotian Zhang, ZhiXin Qin, Yu Kang, Xin Hong, Tingjun Hou
2023 J jnl
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling.
Nat. Mac. Intell.
Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
2023 J jnl
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets.
J. Chem. Inf. Model.
Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huanxiang Liu, Xiaojun Yao, Tingjun Hou, Yu Kang
2023 J jnl
TB-IECS: an accurate machine learning-based scoring function for virtual screening.
J. Cheminformatics
Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan, Yu Kang
2022 J jnl
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction.
J. Chem. Inf. Model.
Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou
2022 J jnl
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation.
J. Chem. Inf. Model.
Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu
2022 J jnl
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands.
J. Chem. Inf. Model.
Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan, Tingjun Hou
2022 J jnl
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism.
J. Chem. Inf. Model.
Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dong-Sheng Cao, Zhe Wang, Tingjun Hou
2022 J jnl
ReMODE: a deep learning-based web server for target-specific drug design.
J. Cheminformatics
Mingyang Wang, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Honglin Li, Chang-Yu Hsieh, Tingjun Hou
2022 J jnl
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.
Briefings Bioinform.
Zhe Wang, Hong Pan, Huiyong Sun, Yu Kang, Huanxiang Liu, Dongsheng Cao, Tingjun Hou
2021 J jnl
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors.
Nucleic Acids Res.
Hongyan Du, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets.
Briefings Bioinform.
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng Cao, Tingjun Hou
2021 J jnl
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction.
J. Cheminformatics
Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dong-Sheng Cao, Tingjun Hou
2020 J jnl
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
J. Chem. Inf. Model.
Ercheng Wang, Hui Liu, Junmei Wang, Gaoqi Weng, Huiyong Sun, Zhe Wang, Yu Kang, Tingjun Hou
2019 J jnl
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods.
Bioinform.
Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou
2018 J jnl
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products.
J. Chem. Inf. Model.
Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou
2017 J jnl
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches.
J. Chem. Inf. Model.
Huiyong Sun, Youyong Li, Mingyun Shen, Dan Li, Yu Kang, Tingjun Hou
2017 J jnl
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
J. Cheminformatics
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou