论文著作

书目章节

[6]. Wei Zhang, Tingjun Hou, Christian Schafmeister, Wilson S. Ross, and David A. Case, Leap and Gleap manual for AmberTools, 2008. [HTML]

[5]. Junmei Wang, Tingjun Hou, Recent advances on in silico ADME modeling, Annual Reports in Computational Chemistry (edited by Ralph wheeler), Elsevier, Volume 5, 2009. (Chapter 5) [HTML]

[4]. Molecular Conceptor courseware, Synergix Ltd. 2008. (contributing the chapter: introduction to chemoinformatics). [HTML]

[3]. Tingjun Hou, Xu Xiaojie, Recent development and application of virtual screening in drug discovery: An Overview. in Frontier in Medicinal Chemistry, Bentham Science Publishers, Vol 3, 2006, 675-703. [HTML]

[2]. Xiaojie Xu, Tingjun Hou, Xuebin Qiao, Wei Zhang, Computer-aided drug design: principle, methods and applications, Chemical Industrial Publisher, 2004. (Chapters 4 to 16)

[1]. Xu Luo, Chemical statistics, Science Publisher, 2002. (Chapter 16)

科研论文

2023年

[478]. 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, Nature Computational Science, 2023, in press, [HTML]

[477]. Odin Zhang, Guangyong Chen, Tingjun Hou, AI-powered structure-based drug design inspired by the lock-and-key model, Nature Computational Science, Research Briefing, 2023, in press, [HTML]

[476]. 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, Nature Computational Science, 2023, 3, 789-804. [HTML]

[475]. 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, Nature Machine Intelligence, 2023, 5, 1020-1030. [HTML]

[474]. Zhenxing Wu, Jike Wang, Hongyan Du, Dejun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dongsheng Cao, Chang-Yu Hsieh*, Tingjun Hou*, Substructure Mask Explanation (SME): an intuitive graph neural network explanation approach for mining structure-activity information from molecular property prediction models, Nature Communications, 2023, 14, 2585. [HTML]

[473]. Weitao Fu, Hao Yang, Chenxian Hu, Jianing Liao, Zhou Gong, Minkui Zhang, Shuai Yang, Shangxiang Ye, Yixuan Lei, Rong Sheng, Zhiguo Zhang, Xiaojun Yao, Chun Tang*, Dan Li*, Tingjun Hou*, Small-Molecule Inhibition of Androgen Receptor Dimerization as a Strategy against Prostate Cancer, ACS Central Science, 2023, 9, 675-684. [HTML]

[472]. Qing Ye, Ruolan Xu, Dan Li, Yu Kang, Yafeng Deng, Feng Zhu, Jiming Chen*, Shibo He, Chang-Yu Hsieh*, Tingjun Hou*, Integrating multi-modal deep learning on knowledge graph for the discovery of synergistic drug combinations against infectious diseases, Cell Reports Physical Science, 2023, 8, 101520. [HTML]

[471]. Hongyan Du, Dejun Jiang, Odin Zhang, Zhenxing Wu, Junbo Gao, Xujun Zhang, Xiaorui Wang, Yafeng Deng, Yu Kang, Dan Li, Peichen Pan*, Chang-Yu Hsieh*, Tingjun Hou*, A Flexible Data-Free Framework for Structure-Based De Novo Drug Design with Reinforcement Learning, Chemical Science, 2023, in press. [HTML]

[470]. Xiaodan Yin, Xiaorui Wang, Yuquan Li, Jike Wang, Yuwei Wang, Yafeng Deng, Tingjun Hou, Huanxiang Liu, Pei Luo, Xiaojun Yao, CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules, Journal of Chemical Information and Modeling, 2023. [HTML]

[469]. Shukai Gu, Huanxiang Liu, Liwei Liu, Tingjun Hou*, Yu Kang*, Artificial intelligence methods in kinase targets profiling: advances and challenges, Drug Discovery Today, 2023. [HTML]

[468]. Xiaorui Wang, Chang-Yu Hsieh*, Xiaodan Yin, Jike Wang, Yuquan Li, Yafeng Deng, Dejun Jiang, Zhenxing Wu, Hongyan Du, Hongming Chen, Yun Li, Huanxiang Liu, Yuwei Wang, Pei Luo, Tingjun Hou*, Xiaojun Yao*, Generic Interpretable Reaction Condition Predictions with Open Reaction Condition Datasets and Unsupervised Learning of Reaction Center, Research, 2023, 6, 0231. [HTML]

[467]. Jian Gao, Zheyuan Shen, Yufeng Xie, Jialiang Lu, Yang Lu, Sikang Chen, Qingyu Bian, Yue Guo, Liteng Shen, Jian Wu, Binbin Zhou, Tingjun Hou, Qiaojun He, Jinxin Che, Xiaowu Dong, TransFoxMol: predicting molecular property with focused attention, Briefings in Bioinformatics, 2023, 24, bbad306. [HTML]

[466]. 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, Journal of Chemical Information and Modeling, 2023, 63, 5232-5243. [HTML]

[465]. 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 in Bioinformatics, 2023, 24, bbad295. [HTML]

[464]. Dejun Jiang, Huifeng Zhao, Hongyan Du, Yafeng Deng, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Jian Wu*, Chang-Yu Hsieh*, Tingjun Hou*, How Good Are Current Docking Programs at Nucleic Acid-Ligand Docking? A Comprehensive Evaluation, Journal of Chemical Theory and Computation, 2023, 66, 10808-10823. [HTML]

[463]. Jieyu Jin, Dong Wang, Guqin Shi, Jingxiao Bao, Jike Wang, Haotian Zhang, Peichen Pan, Dan Li, Xiaojun Yao, Huanxiang Liu, Tingjun Hou*, Yu Kang*, FFLOM: A Flow-Based Autoregressive Model for Fragment-to-Lead Optimization, Journal of Medicinal Chemistry, 2023, 66, 10808-10823. [HTML]

[462]. Chao Shen, Xujun Zhang, Chang-Yu Hsieh, Yafeng Deng, Dong Wang, Lei Xu, Jian Wu, Dan Li, Yu Kang, Tingjun Hou *, Peichen Pan*, A generalized protein-ligand scoring framework with balanced scoring, docking, ranking and screening powers, Chemical Science, 2023, 14, 8129-8146. [HTML]

[461]. 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, Journal of Cheminformatics, 2023, 15, 63. [HTML]

[460]. Xujun Zhang, Chao Shen, Tianyue Wang, Yu Kang, Dan Li, Peichen Pan, Jike Wang, Gaoang Wang, Yafeng Deng, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Zhe Wang*, Topology-Based and Conformation-Based Decoys Database: An Unbiased Online Database for Training and Benchmarking Machine-Learning Scoring Functions, Journal of Medicinal Chemistry, 2023, 66, 9174-9183. [HTML]

[459]. Rongfan Tang, Zhe Wang, Sutong Xiang, Lingling Wang, Yang Yu, Qinghua Wang, Qirui Deng, Tingjun Hou*, and Huiyong Sun*, Uncovering the Kinetic Characteristics and Degradation Preference of PROTAC Systems with Advanced Theoretical Analyses, JACS Au, 2023, 3, 1775-1789. [HTML]

[458]. Qinghua Wang, Zhe Wang, Qirui Deng, Sutong Xiang, Rongfan Tang, Yang Yu, Tingjun Hou*, Haiping Hao*, Huiyong Sun*, Discriminating functional and non-functional nuclear-receptor ligands with a conformational selection-inspired machine learning algorithm, Cell Reports Physical Science, 2023, 8, 101466. [HTML]

[457]. Yang Yu, Zhe Wang, Lingling Wang, Qinghua Wang, Rongfan Tang, Sutong Xiang, Qirui Deng, Tingjun Hou*, Huiyong Sun*, Deciphering the Shared and Specific Drug Resistance Mechanisms of Anaplastic Lymphoma Kinase via Binding Free Energy Computation, Research, 2023, 6, 0170. [HTML]

[456]. Jike Wang, Yundian Zeng, Huiyong Sun, Junmei Wang, Xiaorui Wang, Ruofan Jin, Mingyang Wang, Xujun Zhang, Dongsheng Cao, Xi Chen*, Chang-Yu Hsieh*, Tingjun Hou*, Molecular Generation with Reduced Labeling through Constraint Architecture, Journal of Chemical Information and Modeling, 2023, 63, 3319-3327. [HTML]

[455]. Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu, RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction, Nucleic Acids Research, 2023, 51, W509-W519. [HTML]

[454]. 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, Journal of Chemical Information and Modeling, 2023, 63, 2983-2991. [HTML]

[453]. Suqing Yang, Liuxia Zhang, Youjin Ge, Jinwei Zhang, Jianxin Hu, Chengying Shen, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences, Journal of Cheminformatics, 2023, 15, 48. [HTML]

[452]. Kexin Chen, Guangyong Chen, Junyou Li, Yuansheng Huang, Ercheng Wang, Tingjun Hou, Pheng-Ann Heng, MetaRF: attention-based random forest for reaction yield prediction with a few trails, Journal of Cheminformatics, 2023, 15, 43. [HTML]

[451]. Ziyi Yang, Shaohua Shi, Li Fu, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Matched Molecular Pair Analysis in Drug Discovery: Methods and Recent Applications, Journal of Medicinal Chemistry, 2023, 63, 2345-2359. [HTML]

[450]. Yanjing Duan, Li Fu, Xiaochen Zhang, Tengzhi Long, Yuanhang He, Zhaoqian Liu, Aiping Lu, Yafeng Deng, Chang-Yu Hsieh, Tingjun Hou*, Dongsheng Cao*, Improved GNNs for logD7.4 Prediction by Transferring Knowledge from Low-Fidelity Data,Journal of Chemical Information and Modeling, 2023, 63, 2345-2359. [HTML]

[449]. Haixia Wang, Yueqi Zhang, Jingrui Wang, Yun Chen, Tingjun Hou, Youfu Zhao, Zhonghua Ma, The sphinganine C4-hydroxylase FgSur2 regulates sensitivity to azole antifungal agents and virulence of Fusarium graminearum,Microbiological Research, 2023, 271, 127347. [HTML]

[448]. Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang, Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n‐octanol–water partition coefficient (logP) for druglike molecules using MM‐PBSA method,Journal of Computational Chemistry, 2023, 44, 1300-1311. [HTML]

[447]. Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoag Man, Junmei Wang, Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method,Journal of Computational Chemistry, 2023, 44, 1334-1346. [HTML]

[446]. 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,Journal of Chemical Information and Modeling, 2023, 63, 1133-1142. [HTML]

[445]. Yihao Zhao, Jintu Zhang, Haotian Zhang, Shukai Gu, Yafeng Deng, Yaoquan Tu*, Tingjun Hou*, Yu Kang*, Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems,The Journal of Physical Chemistry Letters, 2023, 14, 4, 1103-1112. [HTML]

[444]. Dejun Jiang, Zhaofeng Ye, Chang-Yu Hsieh, Zhiyi Yang, Xujun Zhang, Yu Kang, Hongyan Du, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Mingyang Wang, Xiaojun Yao, Shengyu Zhang*, Jian Wu*, Tingjun Hou*, MetalProGNet: A Structure-based Deep Graph Model for Metalloprotein-Ligand Interaction Predictions, Chemical Science, 2023, 14, 2054-2069. [HTML]

[443]. Haotian Zhang, Shengming Li, Jintu Zhang, Jike Wang, Dejun Jiang, Zhiwen Bian, Yixue Zhang, Yafeng Deng, Jianfei Song, Yu Kang*, Tingjun Hou*, SDEGen: Learning to Evolve Molecular Conformations from Thermodynamic Noise for Conformation Generation, Chemical Science, 2023, 14, 1557-1568. [HTML]

[442]. Yihao Zhao, Jintu Zhang, Haotian Zhang, Shukai Gu, Yafeng Deng, Yaoquan Tu*, Tingjun Hou*, Yu Kang*, Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems, Journal of Physical Chemistry Letters, 2023, 14, 1103-1112. [HTML]

[441]. Gaoqi Weng, Xuanyan Cai, Dongsheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li*, Tingjun Hou*, PROTAC-DB 2.0: an updated database of PROTACs, Nucleic Acids Research, 2023, 51(D1), D1367-D1372. [HTML]

[440]. Kaiyue Ji, Chong Liu, Zhaoqian Liu, Yafeng Deng, Tingjun Hou*, Dongsheng Cao*, Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?, Briefings in Bioinformatics, 2023, 24, bbad014. [HTML]

[439]. 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 in Bioinformatics, 2023, 24, bbad008. [HTML]

[438]. Xin Chai, Xueping Hu, Xinyue Wang, Huating Wang, Jinping Pang, Wenfang Zhou, Jianing Liao, Luhu Shan, Xiaohong Xu, Lei Xu, Hongguang Xia*, Tingjun Hou*, Dan Li*, Computationally guided discovery of novel non-steroidal AR-GR dual antagonists demonstrating potency against antiandrogen resistance , Acta Pharmacologica Sinica, 2023, 44, 1500-1518. [HTML]

[437]. Fengcheng Li, Jiayi Yin, Mingkun Lu, Minjie Mou, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen, Feng Zhu, DrugMAP: molecular atlas and pharma-information of all drugs, Nucleic Acids Research, 2023, 51(D1), D1288-D1299. [HTML]

[436]. Kuerbannisha Amahong, Wei Zhang, Ying Zhou, Song Zhang, Jiayi Yin, Fengcheng Li, Hongquan Xu, Tianci Yan, Zixuan Yue, Yuhong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han, Feng Zhu, CovInter: interaction data between coronavirus RNAs and host proteins, Nucleic Acids Research, 2023, 51(D1), D546-D556. [HTML]

[435]. Lei Wang, Shaohua Shi, Hui Li, Xiangxiang Zeng, Suyou Liu, Zhaoqian Liu, Yafeng Deng, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Reducing false positive rate of docking-based virtual screening by active learning, Briefings in Bioinformatics, 2023, 24, bbac544. [HTML]

[434]. Lingling Wang, Lei Xu, Zhe Wang, Tingjun Hou*, Haiping Hao*, Huiyong Sun*, Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis, Briefings in Bioinformatics, 2023, 24, bbac544. [HTML]

[433]. Dong Wang, Zhenxing Wu, Chao Shen, Lingjie Bao, Hao Luo, Zhe Wang, Hucheng Yao, Dexin Kong*, Cheng Luo*, Tingjun Hou*, Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors, Briefings in Bioinformatics, 2023, 1, bbac592. [HTML]

[432]. Lei Xu, Xuyang Mu, Minmin Liu, Zhijia Wang, Chao Shen, Qianwen Mu, Bo Feng, Yechun Xu, Tingjun Hou, Lixin Gao, Haini Jiang, Jia Li, Yubo Zhou, Wenlong Wang, Novel thieno [2, 3-b] quinoline-procaine hybrid molecules: A new class of allosteric SHP-1 activators evolved from PTP1B inhibitors, Chinese Chemical Letters, 2023, 34, 108063. [HTML]

[431]. Jialu Wu, Yue Wan, Zhenxing Wu, Shengyu Zhang, Dongsheng Cao*, Chang-Yu Hsieh*, Tingjun Hou*, MF-SuP-pKa: Multi-fidelity modeling with subgraph pooling mechanism for pKa prediction, Acta Pharmaceutica Sinica B, 2023, 13, 2572-2584. [HTML]

[430]. Lingjie Bao, Zhe Wang, Zhenxing Wu, Hao Luo, Jiahui Yu, Yu Kang*, Dongsheng Cao*, Tingjun Hou*, Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach, Acta Pharmaceutica Sinica B, 2023, 13, 54-67. [HTML]

2022年

[429]. 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, Journal of Cheminformatics, 2022, 14, 84. [HTML]

[428]. Tengzhi Long, Shaohua Shi, Shao Liu, Aiping Lu, Zhaoqian Liu, Min Li, Tingjun Hou*, Dongsheng Cao*, Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches, Journal of Chemical Information and Modeling, 2022, 63, 111-125. [HTML]

[427]. Ningning Wang, Xianggui Wang, Guoli Xiong, Ziyi Yang, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes, Journal of Cheminformatics, 2022, 14, 23. [HTML]

[426]. Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dongsheng Cao*, Chang-Yu Hsieh*, Tingjun Hou*, ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction, Journal of Chemical Information and Modeling, 2022, 62, 5975-5987. [HTML]

[425]. Dan Lia, Xiaodong Bao, Jinping Pang, Xueping Hu, Longling Wang, Jiajia Wang, Zhaoxu Yang, Lei Xu, Siyu Wang, Qinjie Weng*, Sunliang Cui*, Tingjun Hou*, Discovery and Optimization of N-acyl-6-sulfonamide-tetrahydroquinoline Derivatives as Novel Non-steroidal Selective Glucocorticoid Receptor Modulators, Journal of Medicinal Chemistry, 2022, 65, 15710-15724. [HTML]

[424]. Xiaochen Zhang, Chengkun Wu*, Jiacai Yi, Xiangxiang Zeng, Canqun Yang, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Pushing the Boundaries of Molecular Property Prediction for Drug Discovery with Multi-task Learning BERT Enhanced by SMILES Enumeration, Research, 2022, 5, 0004. [HTML]

[423]. Tiantian Xu, Qisheng Ma, Yanan Li, Qing Yu, Peichen Pan, Yawen Zheng, Zhijian Li, Xiufang Xiong, Tingjun Hou, Bin Yu, Hongmin Liu, Yi Sun, A small molecule inhibitor of the UBE2F-CRL5 axis induces apoptosis and radiosensitization in lung cancer, Signal Transduction and Targeted Therapy, 2022, 7, 354. [HTML]

[422]. Gaoang Wang, Jiahui Yu, Hongyan Du, Chao Shen, Xujun Zhang, Yifei Liu, Yangyang Zhang, Dongsheng Cao, Peichen Pan*, Tingjun Hou*, VGSC-DB: an online database of voltage-gated sodium channels, Journal of Cheminformatics, 2022, 14, 75. [HTML]

[421]. Gaoang Wang, Lei Xu, Haiyi Chen, Yifei Liu, Peichen Pan*, Tingjun Hou*, Recent advances in computational studies on voltage-gated sodium channels: drug design and mechanism studies , WIRES Computational Molecular Science, 2022, e1641. [HTML]

[420]. Ling Pan, Weidong Tang, Ke Wang, Qifeng Fang, Mengru Liu, Zhanxun Wu, Yi Wang, Sunliang Cui, Gang Hu, Tingjun Hou, Weiwei Hu, Zhong Chen, Xiangnan Zhang, Novel Caspase-1 inhibitor CZL80 improves neurological function in mice after progressive ischemic stroke within a long therapeutic time-window, Acta Pharmacologica Sinica, 2022, 43, 2817-2827. [HTML]

[419]. Jialu Wu, Yu Kang, Peichen Pan*, Tingjun Hou*, Machine learning methods for pKa prediction of small molecules: advances and challenges, Drug Discovery Today, 2022, 27, 103372. [HTML]

[418]. Haixia, Wang, Yun Chen, Tingjun Hou, Yunqing Jia, Zhonghua Ma, The very long-chain fatty acid elongase FgElo2 governs tebuconazole sensitivity and virulence in Fusarium graminearum, Environmental Microbiology, 2022, 24, 5362-5377. [HTML]

[417]. Changwei Chen, Xin Chai, Xueping Hu, Shengying Lou, Dan Li*, Tingjun Hou*, Sunliang Cui*, Discovery of 2-(1-(3-Chloro-4-cyanophenyl)-1H-pyrazol-3-yl)acetamides as Potent, Selective, and Orally Available Antagonists Targeting the Androgen Receptor, Journal of Medicinal Chemistry, 2022, 65, 13074-13093. [HTML]

[416]. Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Min Wu, Tingjun Hou*, Mingli Song*, Root-aligned SMILES: a tight representation for chemical reaction prediction, Chemical Science, 2022, 13, 9023-9034. [HTML]

[415]. Yang Yu, Zhe Wang, Lingling Wang, Sheng Tian, Tingjun Hou*, Huiyong Sun*, Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses, Journal of Cheminformatics, 2022, 14, 56. [HTML]

[414]. Jike Wang, Xiaorui Wang, Huiyong Sun, Mingyang Wang, Yundian Zeng, Dejun Jiang, Zhenxing Wu, Zeyi Liu, Ben Liao, Xiaojun Yao, Chang-Yu Hsieh*, Dongsheng Cao*, Xi Chen*, Tingjun Hou*, ChemistGA: A Chemical Synthesizable Accessible Molecular Generation Algorithm for Real-World Drug Discovery, Journal of Medicinal Chemistry, 2022, 65, 12482-12496. [HTML]

[413]. Qinghua Wang, Zhe Wang, Sheng Tian, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou*, Haiping Hao*, Huiyong Sun*, Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning, Journal of Chemical Information and Modeling, 2022, 62, 3993-4007. [HTML]

[412]. Jie Yu, Xin Chai, Jinping Pang, Zhe Wang, Hong Zhao, Tianli Xie, Lei Xu, Rong Sheng, Dan Li, Su Zeng, Tingjun Hou*, Yu Kang*, Discovery of novel non-nucleoside inhibitors with high potency and selectivity for DNA methyltransferase 3A, European Journal of Medicinal Chemistry, 2022, 114646. [HTML]

[411]. Jiacai Yi, Chengkun Wu, Xiaochen Zhang, Xinyi Xiao, Yanlong Qiu, Wentao Zhao, Tingjun Hou*, Dongsheng Cao*, MICER: a pre-trained encoder-decoder architecture for molecular image captioning, Bioinformatics, 2022, btac545. [HTML]

[410]. Chao Shen, Xujun Zhang, Yafeng Deng, Junbo Gao, Dong Wang, Lei Xu, Peichen Pan*, Tingjun Hou*, Yu Kang*, Boosting Protein-Ligand Binding Pose Prediction and Virtual Screening Based on Residue-Atom Distance Likelihood Potential and Graph Transformer, Journal of Medicinal Chemistry, 2022, 65, 10691-10706. [HTML]

[409]. Xinlei Zhuang, Zhe Wang, Jiansheng Fan, Xuefei Bai, Yingchun Xu, James J Chou, Tingjun Hou, Shuqing Chen, Liqiang Pan, Structure-guided and phage-assisted evolution of a therapeutic anti-EGFR antibody to reverse acquired resistance, Nature Communications, 2022, 3, 1-16. [HTML]

[408]. Hongyan Du, Dejun Jiang, Junbo Gao, Xujun Zhang, Lingxiao Jiang, Yundian Zeng, Zhenxing Wu, Chao Shen, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Peichen Pan*, Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network, Research, 2022, 9873564. [HTML]

[407]. Mingyang Wang, Chang-Yu Hsieh, Jike Wang, Dong Wang, Gaoqi Weng, Chao Shen, Xiaojun Yao, Zhitong Bing, Honglin Li*, Dongsheng Cao*, Tingjun Hou*, RELATION: A Deep Generative Model for Structure-Based De Novo Drug Design, Journal of Medicinal Chemistry, 2022, 65, 9478-9492. [HTML]

[406]. 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, Journal of Chemical Information and Modeling, 2022, 62, 3191-3199. [HTML]

[405]. Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dongsheng Cao, Zhe Wang*, Tingjun Hou*, Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism, Journal of Chemical Information and Modeling, 2022, 62, 2973-2986. [HTML]

[404]. Xujun Zhang, Chao Shen, Ben Liao, Dejun Jiang, Jike Wang, Zhenxing Wu, Hongyan Du, Tianyue Wang, Wenbo Huo, Lei Xu, Dongsheng Cao*, Chang-Yu Hsieh*, Tingjun Hou*, TocoDecoy: A New Approach to Design Unbiased Datasets for Training and Benchmarking Machine-Learning Scoring Functions, Journal of Medicinal Chemistry, 2022, 65, 7918-7932. [HTML]

[403]. 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 in Bioinformatics, 2022, bbac201. [HTML]

[402]. Xueping Hu, Jinping Pang, Changwei Chen, Dejun Jiang, Chao Shen, Xin Chai, Liu Yang, Xujun Zhang, Lei Xu, Sunliang Cui, Tingjun Hou, Dan Li*, Discovery of novel non-steroidal selective glucocorticoid receptor modulators by structure-and IGN-based virtual screening, structural optimization, and biological evaluation, European Journal of Medicinal Chemistry, 2022, 237, 114382. [HTML]

[401]. Ningning Wang, Xianggui Wang, Guoli Xiong, Ziyi Yang, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes, Journal of Cheminformatics, 2022, 14, 23. [HTML]

[400]. Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Changyu Hsieh*, Dongsheng Cao*, Tingjun Hou*, Knowledge-based BERT: a method to extract molecular features like computational chemists, Briefings in Bioinformatics, 2022, 23, bbac131. [HTML]

[399]. Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao*, Tingjun Hou*, Huiyong Sun*, Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations, Briefings in Bioinformatics, 2022, 23, bbac127. [HTML]

[398]. Renhong Yan, Enjun Xie, Yaning Li, Jin Li, Yuanyuan Zhang, Ximin Chi, Xueping Hu, Lei Xu, Tingjun Hou, Brent R. Stockwell, Junxia Min, Qiang Zhou & Fudi Wang, The structure of erastin-bound xCT-4F2hc complex reveals molecular mechanisms underlying erastin-induced ferroptosis, Cell Research, 2022, 32, 687–690. [HTML]

[397]. Xiaochen Zhang, Jiacai Yi, Guoping Yang, Chengkun Wu, Tingjun Hou*, Dongsheng Cao*, ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images, Briefings in Bioinformatics, 2022, 23, bbac033. [HTML]

[396]. Rui Shi, Peichen Pan, Rui Lv, Chongqing Ma, Enhui Wu, Ruochen Guo, Zhihao Zhao, Hexing Song, Joe Zhou, Yang Liu, Guoqiang Xu, Tingjun Hou*, Zhenhui Kang*, Jian Liu*, High-throughput glycolytic inhibitor discovery targeting glioblastoma by graphite dots-assisted LDI mass spectrometry, Science Advances, 2022, 8, eabl4923. [HTML]

[395]. Jinping Pang, Xueping Hu, Yunxia Wang, Jianing Liao, Xin Chai, Xuwen Wang, Chao Shen, Jiajia Wang, Lulu Zhang, Xinyue Wang, Feng Zhu, Qinjie Weng, Lei Xu, Tingjun Hou, Dan Li*, Discovery of a novel nonsteroidal selective glucocorticoid receptor modulator by virtual screening and bioassays, Acta Pharmacologica Sinica, 2022, 43, 2429–2438. [HTML]

[394]. Xin Chai, Huiyong Sun, Wenfang Zhou, Changwei Chen, Luhu Shan, Yuhui Yang, Junzhao He, Jinping Pang, Liu Yang, Xinyue Wang, Sunliang Cui, Yaqin Fu, Xiaohong Xu, Lei Xu, Xiaojun Yao, Dan Li*, Tingjun Hou*, Discovery of N-(4-(Benzyloxy)-phenyl)-sulfonamide Derivatives as novel antagonists of the human androgen receptor targeting the activation function 2, Journal of Medicinal Chemistry, 2022, 65, 2507-2521. [HTML]

[393]. Dejun Jiang, Huiyong Sun, Jike Wang, Changyu Hsieh, Yuquan Li, Zhenxing Wu, Dongsheng Cao*, Jian Wu*, Tingjun Hou*, Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning, Briefings in Bioinformatics, 2022, 23, bbab597. [HTML]

[392]. Guoli Xiong, Zhijiang Yang, Jiacai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety, Nucleic Acids Research, 2022, 50(D1), D1200-D1207. [HTML]

[391]. Mingyang Wang, Huiyong Sun, Jike Wang, Jinping Pang, Xin Chai, Lei Xu, Honglin Li*, Dongsheng Cao*, Tingjun Hou*, Comprehensive assessment of deep generative architectures for de novo drug design, Briefings in Bioinformatics, 2022, 23, bbab544. [HTML]

[390]. Jinping Pang, Chao Shen, Wenfang Zhou, Yunxia Wang, Luhu Shan, Xin Chai, Ying Shao, Xueping Hu, Feng Zhu, Danyan Zhu, Li Xiao, Lei Xu, Xiaohong Xu, Dan Li*, Tingjun Hou*, Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays, Acta Pharmacologica Sinica, 2022, 43, 229-239. [HTML]

[389]. Mingyang Wang, Zhe Wang, Huiyong Sun, Jike Wang, Chao Shen, Gaoqi Weng, Xin Chai, Honglin Li*, Dongsheng Cao*, Tingjun Hou*, Deep learning approaches for de novo drug design: an overview, Current Opinion in Structural Biology, 2022, 72, 135-144. [HTML]

[388]. 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, Journal of Chemical Information and Modeling, 2022, 62, 5233-5245. [HTML]

[387]. Xueping Hu, Liu Yang, Xin Chai, Yixuan Lei, Md Shah Alam, Lu Liu, Chao Shen, Dejun Jiang, Zhe Wang, Zhiyong Liu, Lei Xu, Kanglin Wan, Tianyu Zhang, Yuelan Yin, Dongsheng Cao*, Dan Li*, Tingjun Hou*, Discovery of novel DprE1 inhibitors via computational bioactivity fingerprints and structure-based virtual screening, Acta Pharmacologica Sinica, 2022, 43, 1605–1615. [HTML]

[386]. Yu Zhang, Lei Xu, Yao Zhang, Jie Pan, Pu-qing Wang, Sheng Tian, Huan-ting Li, Bowen Gao, Tingjun Hou*, Xuechu Zhen*, Longtai Zheng*, Discovery of novel MIF inhibitors that attenuate microglial inflammatory activation by structures-based virtual screening and in vitro bioassays, Acta Pharmacologica Sinica, 2022, 43, 1508–1520. [HTML]

[385]. Liu Yang, Xueping Hu, Xin Chai, Qing Ye, Jinping Pang, Dan Li*, Tingjun Hou*, Opportunities for overcoming tuberculosis: emerging targets and their inhibitors, Drug Discovery Today, 2022, 27, 326-336. [HTML]

[384]. Xueping Hu, Jinping Pang, Jintu Zhang, Chao Shen, Xin Chai, Ercheng Wang, Haiyi Chen, Xuwen Wang, Mojie Duan, Weitao Fu, Lei Xu, Yu Kang, Dan Li*, Hongguang Xia*, Tingjun Hou*, Discovery of novel GR ligands towards druggable GR antagonist conformations identified by MD Simulations and Markov state model analysis, Advanced Science, 2022, 9, 2102435. [HTML]

软件著作权

[22]. 电压门控钠离子通道在线数据平台，2022SR1424394

[21]. DeepCoSI共价结合位点在线预测平台，2022SR0318406

[20]. CovalentInDB共价抑制剂在线数据平台，2021SR1188113

[19]. 在线AI打分系统及虚拟筛选系统PLIC，2021SR0530537

[18]. 在线描述符生成及基于AI的打分函数构建平台软件，2020SR0243860

[17]. HawkDock蛋白-蛋白对接计算在线计算平台软件，2018SR733536

[16]. 曹东升、陈翔等，数据驱动的分子警示子结构挖掘软件 V1.0，2021SR0278764

发明专利

[24]. 李阳，盛荣，富炜涛，胡陈娴，杨浩，张珉魁，廖佳宁，噻二唑酰胺类化合物及其应用，申请号：CN202110870155.0，授权公告号：CN113444081B，授权公告日：2022.07.05

[23]. 刘坚，石瑞，潘培辰，吕蕊，康振辉，一种己糖激酶2抑制剂的筛选方法和小分子化合物在制备抗肿瘤药物中的应用，申请号：CN202110429488.X，授权公告号：CN113109418B，授权公告日：2022.09.09

[22]. 李丹 富炜涛 张珉魁 盛荣 汤钦，苯并吡喃酮或喹啉酮类化合物及其应用，申请号：CN202010413885.3，授权公告号：CN111533721B，授权公告日：2022.04.26

[21]. 康玉，，余洁，谢天立，曾苏，DNA甲基转移酶3A抑制剂及其应用，申请号：CN202010067400.X，授权公告号：CN111281873B，授权公告日：2021.01.26

[7]. 余慧东，沈明云，潘培辰，一种化合物在制备治疗乳腺癌药物中的应用，申请号：201310248134.0，授权公告号：103316002B，授权公告日：2015.04.15

[6]. 余慧东，沈明云，潘培辰，一种化合物在制备治疗白血病药物中的应用，申请号：ZL201210154752.4，授权公告号：102697782B，授权公告日：2013.09.18

[5]. 余慧东，沈明云，潘培辰，李铭源，黎晌，4，7-二氢四唑[1，5-α]嘧啶类化合物及其衍生物在制备预防或治疗脑出血药物中的应用，申请号：201210123287.8，授权公告号：102432612B，授权公告日：2014.09.17

[4]. 余慧东，沈明云，潘培辰，李有勇，周顺烨，4,7-二氢四唑[1,5-a]嘧啶衍生物及其在制备抗肿瘤药物中的应用，申请号：ZL201110263953.3，授权公告号：102432612B，授权公告日：2015.07.08

[3]. 余慧东 沈明云 潘培辰 李有勇 周顺晔，3-[4-(磺酰)苯]脲类化合物在制备抗肿瘤药物中的应用，申请号：CN201110263951.4，授权公告号：CN102327275B，授权公告日：2013.03.20

[2]. 余慧东，沈明云，潘培辰，李有勇，周顺晔，一种小分子化合物在制备抗肺癌药物中的应用，申请号：ZL201110263589.0，授权公告号：102389430B，授权公告日：2013.08.28

[1]. Ming-Yuen Lee, Tingjun Hou, Huidong Yu, Method of treating and/or preventing neurodegenerative diseases, US20160113931, Filed: Oct. 23, 2015