Yu Kang

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 33

Top Topics

Molecular Dynamics Simulations

Virtual Screening

Predicting Protein

Top Venues

J. Chem. Inf. Model.

Briefings Bioinform.

J. Cheminformatics

Publications

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
Token-Mol 1.0: Tokenized drug design with large language model. CoRR (2024)
Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. J. Chem. Inf. Model. 64 (6) (2024)
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
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. 64 (4) (2024)
Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences. Briefings Bioinform. 25 (4) (2024)
Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. J. Chem. Inf. Model. 64 (13) (2024)
Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh
A general model for predicting enzyme functions based on enzymatic reactions. J. Cheminformatics 16 (1) (2024)
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
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. CoRR (2024)
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
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. J. Chem. Inf. Model. 64 (14) (2024)
Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. J. Chem. Inf. Model. 64 (9) (2024)
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
Learning on topological surface and geometric structure for 3D molecular generation. Nat. Comput. Sci. 3 (10) (2023)
Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Tingjun Hou, Peichen Pan
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Briefings Bioinform. 24 (5) (2023)
Jintu Zhang, Haotian Zhang, Zhixin Qin, Yu Kang, Xin Hong, Tingjun Hou
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. J. Chem. Inf. Model. 63 (4) (2023)
Haiyi Chen, Yue Guo, Shengqing Ye, Jintu Zhang, Haotian Zhang, Na Liu, Rui Zhou, Tingjun Hou, Hongguang Xia, Yu Kang, Mojie Duan
On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J. Chem. Inf. Model. 63 (16) (2023)
Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huanxiang Liu, Xiaojun Yao, Tingjun Hou, Yu Kang
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. J. Chem. Inf. Model. 63 (21) (2023)
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
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. Nat. Mac. Intell. 5 (9) (2023)
Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu, Zhe Wang, Tingjun Hou, Yu Kang
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? Briefings Bioinform. 24 (2) (2023)
Xujun Zhang, Chao Shen, Dejun Jiang, Jintu Zhang, Qing Ye, Lei Xu, Tingjun Hou, Peichen Pan, Yu Kang
TB-IECS: an accurate machine learning-based scoring function for virtual screening. J. Cheminformatics 15 (1) (2023)
Yuwei Yang, Chang-Yu Hsieh, Yu Kang, Tingjun Hou, Huanxiang Liu, Xiaojun Yao
Deep Generation Model Guided by the Docking Score for Active Molecular Design. J. Chem. Inf. Model. 63 (10) (2023)
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
Efficient and accurate large library ligand docking with KarmaDock. Nat. Comput. Sci. 3 (9) (2023)
Zhe Wang, Hong Pan, Huiyong Sun, Yu Kang, Huanxiang Liu, Dongsheng Cao, Tingjun Hou
fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. Briefings Bioinform. 23 (5) (2022)
Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dong-Sheng Cao, Zhe Wang, Tingjun Hou
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. J. Chem. Inf. Model. 62 (12) (2022)
Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. J. Chem. Inf. Model. 62 (13) (2022)
Mingyang Wang, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Honglin Li, Chang-Yu Hsieh, Tingjun Hou
ReMODE: a deep learning-based web server for target-specific drug design. J. Cheminformatics 14 (1) (2022)
Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan, Tingjun Hou
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. J. Chem. Inf. Model. 62 (21) (2022)
Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. J. Chem. Inf. Model. 62 (23) (2022)
Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng Cao, Tingjun Hou
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. 22 (4) (2021)
Hongyan Du, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao, Tingjun Hou
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic Acids Res. 49 (Database-Issue) (2021)
Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dong-Sheng Cao, Tingjun Hou
The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction. J. Cheminformatics 13 (1) (2021)
Ercheng Wang, Hui Liu, Junmei Wang, Gaoqi Weng, Huiyong Sun, Zhe Wang, Yu Kang, Tingjun Hou
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. J. Chem. Inf. Model. 60 (11) (2020)
Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinform. 35 (10) (2019)
Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. J. Chem. Inf. Model. 58 (6) (2018)
Huiyong Sun, Youyong Li, Mingyun Shen, Dan Li, Yu Kang, Tingjun Hou
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. J. Chem. Inf. Model. 57 (8) (2017)
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J. Cheminformatics 9 (1) (2017)