Book Chapters

[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]

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

---

Papers

2024

[528]. Zhenxing Wu, Odin Zhang, Xiaorui Wang, Li Fu, Huifeng Zhao, Jike Wang, Hongyan Du, Dejun Jiang, Yafeng Deng, Dongsheng Cao*, Chang-Yu Hsieh*, Tingjun Hou*, Leveraging Language Model for Advanced Multi-Property Molecular Optimization via Prompt Engineering, Nature Machine Intelligence, 2024, accepted, [HTML]

[527]. Mingyang Wang, Shuai Li, Jike Wang, Odin Zhang, Hongyan Du, Dejun Jiang, Zhenxing Wu, Yafeng Deng, Yu Kang, Peichen Pan, Dan Li, Xiaorui Wang, Tingjun Hou*, Chang-Yu Hsieh*, ClickGen: Directed Exploration of Synthesizable Chemical Space Leading to the Rapid Synthesis of Novel and Active Lead Compounds via Modular Reactions and Reinforcement Learning, Nature Communications, 2024, accepted, [HTML]

[526]. Xiaorui Wang, Xiaodan Yin, Dejun Jiang, Huifeng Zhao, Zhenxing Wu, Odin Zhang, Jike Wang, Yuquan Li, Yafeng Deng, Huanxiang Liu, Pei Luo, Yuqiang Han, Tingjun Hou*, Xiaojun Yao*, Chang-Yu Hsieh*, Multi-Modal Deep Learning Enables Ultrafast and Accurate Annotation of Enzymatic Active Sites, Nature Communications, 2024, 15, 7348, [HTML]

[525]. Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Tingjun Hou*, Qiang Zhang*, Huajun Chen*, Retrosynthesis prediction with an iterative string editing model, Nature Communications, 2024, 15, 6404, [HTML]

[524]. Jingxuan Ge, Shimeng Li, Gaoqi Weng, Huating Wang, Meijing Fang, Huiyong Sun, Yafeng Deng, Chang-Yu Hsieh, Dan Li*, Tingjun Hou*, PROTAC-DB 3.0: an Updated Database of PROTACs with Extended Pharmacokinetic Parameters, Nucleic Acids Research, 2024, in press, [HTML]

[523]. Jie Yue, Bingxin Peng, Yu Chen, Jieyu Jin, Xinda Zhao, Chao Shen, Xiangyang Ji, Chang-Yu Hsieh, Jianfei Song, Tingjun Hou*, Yafeng Deng*, Jike Wang*, Unlocking comprehensive molecular design across all scenarios with large language model and unordered chemical language, Chemical Science, 2024, in press, [HTML]

[522]. Lei Zhang, Di Ke, Yuting Li, Hui Zhang, Xi Zhang, Sihan Wang, Shaokai Ni, Bo Peng, Huixuan Zeng, Tingjun Hou, Yushen Du, Peichen Pan, Yongping Yu, Wenteng Chen, Design and synthesis of 7-membered lactam fused hydroxypyridinones as potent metal binding pharmacophores (MBPs) for inhibiting influenza virus PAN endonuclease, European Journal of Medicinal Chemistry, 2024, 276, 116639, [HTML]

[521]. Qirui Deng, Zhe Wang, Sutong Xiang, Qinghua Wang, Yifei Liu, Tingjun Hou*, Huiyong Sun*, RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning, Journal of Chemical Information and Modeling, 2024, in press, [HTML]

[520]. Tianyue Wang, Xujun Zhang, Odin Zhang, Guangyong Chen, Peichen Pan, Ercheng Wang, Jike Wang, Jialu Wu, Donghao Zhou, Langcheng Wang, Ruofan Jin, Shicheng Chen, Chao Shen, Yu Kang*, Chang-Yu Hsieh*, Tingjun Hou*, Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop, Research, 2024, 7, 0408, [HTML]

[519]. Hanyu Zhang, Yuan Zhou, Zhichao Zhang, Huaicheng Sun, Ziqi Pan, Minjie Mou, Wei Zhang, Qing Ye, Tingjun Hou, Honglin Li, Chang-Yu Hsieh, Feng Zhu, Large Language Model-Based Natural Language Encoding Could Be All You Need for Drug Biomedical Association Prediction, Analytical Chemistry, 2024, 96, 12395-12403, [HTML]

[518]. 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, Journal of Chemical Information and Modeling, 2024, 64, 5016-5027, [HTML]

[517]. Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dongsheng 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, Journal of Chemical Information and Modeling, 2024, 64, 5381-5391, [HTML]

[516]. 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 in Bioinformatics, 2024, 25, bbae304, [HTML]

[515]. Shaohua Shi, Li Fu, Jiacai Yi, Ziyi Yang, Xiaochen Zhang, Youchao Deng, Wenxuan Wang, Chengkun Wu, Wentao Zhao, Tingjun Hou, Xiangxiang Zeng, Aiping Lyu, Dongsheng Cao, ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery, Nucleic Acids Research, 2024, 52(W1), W439, [HTML]

[514]. Xiaohong Zhu, Mengqi Luo, Ke An, Danfeng Shi, Tingjun Hou*, Arieh Warshel*, Chen Bai*, Exploring the activation mechanism of metabotropic glutamate receptor 2, Proceedings of the National Academy of Sciences, 2024, 121, e2401079121, [HTML]

[513]. Xiaoyan Xu, Tingxue Xie, Mengxin Zhou, Yaqin Sun, Fengqi Wang, Yanan Tian, Ziyan Chen, Yanqi Xie, Ronghai Wu, Xufeng Cen, Jichun Zhou, Tingjun Hou, Lei Zhang, Chaoyang Huang, Qingwei Zhao, Dongrui Wang, Hongguang Xia, Hsc70 promotes anti-tumor immunity by targeting PD-L1 for lysosomal degradation, Nature Communications, 2024, 15, 4237, [HTML]

[512]. Haiyi Chen, Yu Shi, Man Huang, Ting Lu, Huimin Zhang, Chun Zhou*, Tingjun Hou*, Youjun Feng*, Recognition and acquisition of FakB2-loaded exogenous fatty acid (eFA) by a streptococcal FakA kinase, Science bulletin, 2024, in press, [HTML]

[511]. Xinyue Wang, Xin Chai, Luhu Shan, Xiaohong Xu, Lei Xu, Tingjun Hou, Huiyong Sun*, Dan Li*, A potent new-scaffold androgen receptor antagonist discovered on the basis of a MIEC-SVM model, Acta Pharmacologica Sinica, 2024, 45, 1978-1991, [HTML]

[510]. Jintu Zhang, Odin Zhang, Luigi Bonati*, Tingjun Hou*, Combining transition path sampling with data-driven collective variables through a reactivity-biased shooting algorithm, Journal of Chemical Theory and Computation, 2024, 10, 45234532, [HTML]

[509]. Xujun Zhang, Chao Shen, Chang-Yu Hsieh*, Tingjun Hou*, Harnessing deep learning for enhanced ligand docking, Trends in Pharmacological Sciences, 2024, 45, 103-106, [HTML]

[507]. Jingxuan Ge, Dejun Jiang, Huiyong Sun, Yu Kang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh*, Tingjun Hou*, Deep-learning-based prediction framework for protein-peptide interactions with structure generation pipeline, Cell Reports Physical Science, 2024, 5, 101980, [HTML]

[506]. Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Peifei Nie, Aiping Lu, Chengkun Wu, Yafeng Deng, Changyu Hsieh, Xiangxiang Zeng, Tingjun Hou*, Dongsheng Cao*, OptADMET: an open substructure modification guiding workspace for multiple ADMET property optimization, Nature Protocols, 2024, 19, 1105-1121, [HTML]

[505]. Renling Hu, Jintu Zhang, Yu Kang, Zhe Wang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh*, Tingjun Hou*, Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization, Journal of Chemical Theory and Computation, 2024, 20, 1465-1478, [HTML]

[504]. Haiyi Chen, Yuxin Zhou, Xinyue Wang, Xin Chai, Zhe Wang, Ercheng Wang, Lei Xu, Tingjun Hou*, Dan Li*, Mojie Duan*, Discovery of Novel Anti‐Resistance AR Antagonists Guided by Funnel Metadynamics Simulation, Advanced Science, 2024, 11, 2309261, [HTML]

[503]. Li Fu, Shaohua Shi, Jiacai Yi, Ningning Wang, Yuanhang He, Zhenxing Wu, Jinfu Peng, Youchao Deng, Wenxuan Wang, Chengkun Wu, Aiping Lyu, Xiangxiang Zeng, Wentao Zhao, Tingjun Hou*, Dongsheng Cao*, ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support, Nucleic Acids Research, 2024, 52(W1), W422-W431, [HTML]

[502]. Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou*, Chang-Yu Hsieh*, A general model for predicting enzyme functions based on enzymatic reactions, Journal of Cheminformatics, 2024, 16, 38, [HTML]

[501]. Kepeng Chen, Ruolan Xu, Xueping Hu, Dan Li, Tingjun Hou*, Yu Kang*, Recent advances in the development of DprE1 inhibitors using AI/CADD approaches, Drug Discovery Today, 2024, 29, 103987, [HTML]

[500]. Tianhao Wang, Jianbo Tong*, Xing Zhang, Zhe Wang, Lei Xu, Peichen Pan*, Tingjun Hou*, Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain, Computers in Biology and Medicine, 2024, 174, 108397, [HTML]

[499]. 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, Journal of Chemical Information and Modeling, 2024, 64, 3630-3639, [HTML]

[498]. 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, Journal of Chemical Information and Modeling, 2024, 64, 2112-2124, [HTML]

[497]. Hongyan Du, Guo-Wei Wei*, Tingjun Hou, Multiscale topology in interactomic network: From transcriptome to antiaddiction drug repurposing, Briefings in Bioinformatics, 2024, 25, bbae054, [HTML]

[496]. Shukai Gu, Lingjie Bao, Yuwei Yang, Yihao Zhao, Henry Hoi Yee Tong, Liwei Liu, Huanxiang Liu*, Tingjun Hou*, Yu Kang*, AMGC is a multiple-task graph neutral network for epigenetic target profiling, Cell Reports Physical Science, 2024, 5, 101850, [HTML]

[495]. 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*, GARel: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space, Journal of Chemical Information and Modeling, 2024, 64, 1213-1228, [HTML]

[494]. Siyuan Chen, Yao Liu, Zhe Wang, Chengcheng Qi, Yanzhen Yu, Lei Xu, Tingjun Hou*, Rong Sheng*, Identification of 3-aryl-5-methyl-isoxazole-4-carboxamide derivatives and analogs as novel HIF-2α agonists through docking-based virtual screening and structural modification, European Journal of Medicinal Chemistry, 2024, 268, 116227, [HTML]

[493]. Yiheng Zhu, Jialu Wu, Chaowen Hu, Jiahuan Yan, Kim Hsieh*, Tingjun Hou*, Jian Wu*, Sample-efficient Multi-objective Molecular Optimization with GflowNets, Advances in Neural Information Processing Systems 36 (NeurIPS 2023), [HTML]

[492]. Liu Yang, Xueping Hu, Yang Lu, Ruolan Xu, Yaping Xu, Wanli Ma, Md Shah Alam, Tianyu Zhang, Xin Chai, Yixuan Lei, Qing Ye, Xiaowu Dong, Yu Kang, Jinxin Che*, Tingjun Hou*, Dan Li*, Discovery of N-(1-(6-oxo-1,6-dihydropyrimidine)-pyrazole) Acetamide Derivatives as Novel Noncovalent DprE1 Inhibitors against Mycobacterium tuberculosis, Journal of Medicinal Chemistry, 2024, 67, 1914-1931, [HTML]

[491]. Heng Cai, Chao Shen, Tianye Jian, Xujun Zhang, Tong Chen, Xiaoqi Han, Zhuo Yang, Wei Dang, Chang-Yu Hsieh, Yu Kang, Peichen Pan, Xiangyang Ji, Jianfei Song*, Tingjun Hou*, Yafeng Deng*, CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training, Chemical Science, 2024, 15, 1449-1471, [HTML]

[490]. 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*, Comprehensive Assessment of Protein Loop Modeling Programs on Large-scale Datasets: Prediction Accuracy and Efficiency, Briefings in Bioinformatics, 2024, 25, bbad486, [HTML]

[489]. Dejun Jiang, Hongyan Du, Huifeng Zhao, Yafeng Deng, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Ercheng Wang, Tingjun Hou*, Chang-Yu Hsieh*, Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes, Physical Chemistry Chemical Physics, 2024, 26, 10323-10335, [HTML]

[488]. Xiaodan Yin, Chang-Yu Hsieh*, Xiaorui Wang, Zhenxing Wu, Qing Ye, Yafeng Deng, Hongming Chen, Pei Luo, Huanxiang Liu, Tingjun Hou*, Xiaojun Yao*, Enhancing Generic Reaction Yield Prediction through Reaction Condition-Based Contrastive Learning, Research, 2024, 7, 0292, [HTML]

[487]. Gaoqi Weng, Huifeng Zhao, Dou Nie, Haotian Zhang, Liwei Liu*, Tingjun Hou*, Yu Kang*, RediscMol: Benchmarking molecular generation models in biological properties, Journal of Medicinal Chemistry, 2024, 67, 1533-1543, [HTML]

[486]. Haiyang Zhong, Xinyue Wang, Shicheng Chen, Zhe Wang, Huating Wang, Lei Xu, Tingjun Hou, Xiaojun Yao, Dan Li, Peichen Pan, Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design, Journal of Medicinal Chemistry, 2024, 67, 138-151, [HTML]

[485]. Xing Zhang, Jianbo Tong, Tianhao Wang, Tianyue Wang, Lei Xu, Zhe Wang, Tingjun Hou, Peichen Pan, Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis, Computers in Biology and Medicine, 2024, 169, 107815, [HTML]

[484]. Zipeng Zhong, Jie Song, Zunlei Feng, Tiantao Liu, Lingxiang Jia, Shaolun Yao, Tingjun Hou, Mingli Song, Recent advances in deep learning for retrosynthesis, Wiley interdisciplinary reviews: Computational Molecular Science, 2024, 14, e1694, [HTML]

2023

[483]. 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, 3, 849-859, [HTML]

[482]. 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, 3, 827-828, [HTML]

[481]. 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]

[480]. 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]

[479]. 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]

[478]. 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]

[477]. Zhenxing Wu, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh*, Tingjun Hou*, From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery, Journal of Chemical Information and Modeling, 2023, 63, 7617-7627. [HTML]

[476]. Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou*, Haiping Hao*, Huiyong Sun*, Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling, Journal of Chemical Information and Modeling, 2023, 63, 7529-7544. [HTML]

[475]. 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]

[474]. 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, 14, 12166-12181. [HTML]

[473]. 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, Journal of Chemical Information and Modeling, 2023, 63, 6525-6536. [HTML]

[472]. Yiheng Zhu, Zhenqiu Ouyang, Ben Liao, Jialu Wu, Yixuan Wu, Chang-Yu Hsieh*, Tingjun Hou*, Jian Wu*, MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation, Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI2023), 2023, 5002-5010. [HTML]

[471]. Yunxia Wang, Ziqi Pan, Minjie Mou, Weiqi Xia, Hongning Zhang, Hanyu Zhang, Jin Liu, Lingyan Zheng, Yongchao Luo, Hanqi Zheng, Xinyuan Yu, Xichen Lian, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu, A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder, Nucleic Acids Research, 2023, 21, e110. [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, 63, 6169-6176. [HTML]

[469]. Min Li, Huijuan Yu, Yiran Li, Xin Li, Shiqing Huang, Xiaogang Liu, Gaoqi Weng, Lei Xu, Tingjun Hou, Dong-Sheng Guo, Yi Wang, Rational design of supramolecular self-assembly sensor for living cell imaging of HDAC1 and its application in high-throughput screening, Biosensors and Bioelectronics, 2023, 242, 115716. [HTML]

[468]. Shukai Gu, Huanxiang Liu, Liwei Liu, Tingjun Hou*, Yu Kang*, Artificial intelligence methods in kinase targets profiling: advances and challenges, Drug Discovery Today, 2023, 28, 103796. [HTML]

[467]. 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]

[466]. 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]

[465]. 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]

[464]. 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]

[463]. 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]

[462]. 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]

[461]. 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]

[460]. 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]

[459]. 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]

[458]. 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]

[457]. 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]

[456]. 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]

[455]. 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]

[454]. 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]

[453]. 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]

[452]. 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]

[451]. 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]

[450]. 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]

[449]. 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]

[448]. 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]

[447]. 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]

[446]. 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]

[445]. 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]

[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

[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, in press. [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]

2021

[383]. Dejun Jiang, Chang-Yu Hsieh, Zhenxing Wu, Yu Kang, Jike Wang, Ercheng Wang, Ben Liao, Chao Shen, Lei Xu, Jian Wu*, Dongsheng Cao*, Tingjun Hou*, InteractionGraphNet: a novel and efficient deep graph representation learning framework for accurate protein-ligand interaction predictions, Journal of Medicinal Chemistry, 2021, 64, 18209-18232. [HTML]

[382]. Ziyi Yang, Li Fu, Aiping Lu, Shao Liu, Tingjun Hou*, Dongsheng Cao*, Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion, Journal of Cheminformatics, 2021, 13, 86. [HTML]

[381]. Chao Shen, Xueping Hu, Junbo Gao, Xujun Zhang, Haiyang Zhong, Zhe Wang, Lei Xu, Yu Kang, Dongsheng Cao*, Tingjun Hou*, The impact of cross-docked poses on performance of machine learning classifier for protein-ligand binding pose prediction, Journal of Cheminformatics, 2021, 13, 81. [HTML]

[380]. Weitao Fu, Minkui Zhang, Jianing Liao, Qing Tang, Yixuan Lei, Zhou Gong, Luhu Shan, Mojie Duan, Xin Chai, Jinping Pang, Chun Tang, Xuwen Wang, Xiaohong Xu, Dan Li*, Rong Sheng*, Tingjun Hou*, Discovery of a novel androgen receptor antagonist manifesting evidence to disrupt the dimerization of the ligand-binding domain via attenuating the hydrogen-bonding network, Journal of Medicinal Chemistry, 2021, 64, 17221-17238. [HTML]

[379]. Qing Ye, Chang-Yu Hsieh, Ziyi Yang, Yu Kang, Jiming Chen, Dongsheng Cao*, Shibo He*, Tingjun Hou*, A unified drug-target interaction prediction framework based on knowledge graph and recommendation system, Nature Communications, 2021, 12, 6775. [HTML]

[378]. Gaoqi Weng, Dan Li, Yu Kang*, Tingjun Hou*, Integrative modeling of PROTAC-mediated ternary complexes, Journal of Medicinal Chemistry, 2021, in press. [HTML]

[377]. Jike Wang, Chang-Yu Hsieh, Mingyang Wang, Xiaorui Wang, Zhenxing Wu, Dejun Jiang, Benben Liao, Xujun Zhang, Bo Yang, Qiaojun He, Dongsheng Cao*, Xi Chen*, Tingjun Hou*, Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning, Nature Machine Intelligence, 2021, 3, 914-922. [HTML]

[376]. Haiyi Chen, Yu Kang, Mojie Duan*, Tingjun Hou*, Regulation Mechanism for the Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II, The Journal of Physical Chemistry Letters, 2021, 12, 6252-6261. [HTML]

[375]. Weitao Fu, Ercheng Wang, Di Ke, Hao Yang, Lingfeng Chen, Jingjing Shao, Xueping Hu, Lei Xu, Na Liu*, Tingjun Hou*, Discovery of a Novel Fusarium Graminearum Mitogen-activated Protein Kinase (FgGpmk1) Inhibitor for the Treatment of Fusarium Head Blight, Journal of Medicinal Chemistry, 2021, 64, 13841-13852. [HTML]

[374]. Huibing Zhang, Linan Chen, Dehua Yang, Chunyou Mao, Qingya Shen, Wenbo Feng, Dandan Shen, Antao Dai, Shanshan Xie, Yan Zhou, Jiao Qin, Jinpeng Sun, Daniel H. Scharf, Tingjun Hou, Tianhua Zhou, Mingwei Wang, Yan Zhang, Structural insights into ligand recognition and activation of the melanocortin-4 receptor, Cell Research, 2021, 31, 1163-1175. [HTML]

[373]. Chengkun Wu, Xiaochen Zhang, Zhijiang Yang, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules, Briefings in Bioinformatics, 2021, 22, bbab327. [HTML]

[372]. Guoli Xiong, Chao Shen, Ziyi Yang, Dejun Jiang, Shao Liu, Aiping Lu, Xiang Chen, Tingjun Hou*, Dongsheng Cao*, Featurization strategies for protein–ligand interactions and their applications in scoring function development, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021, e1567. [HTML]

[371]. Xiaoyan Xu, Yaqin Sun, Xufeng Cen, Bing Shan, Qingwei Zhao, Tingxue Xie, Zhe Wang, Tingjun Hou, Yu Xue, Mengmeng Zhang, Di Peng, Qiming Sun, Cong Yi, Ayaz Najafov, Hongguang Xia, Metformin activates chaperone-mediated autophagy and improves disease pathologies in an Alzheimer disease mouse model, Protein & Cell, 2021, 12, 769-787. [HTML]

[370]. Yanan Li, Chaorong Wang, Tiantian Xu, Peichen Pan, Qing Yu, Lei Xu, Xiufang Xiong, Tingjun Hou, Sunliang Cui, Yi Sun, Discovery of a small molecule inhibitor of cullin neddylation that triggers ER stress to induce autophagy, Acta Pharmaceutica Sinica B, 2021, 11, 3567-3584. [HTML]

[369]. Ercheng Wang, Weitao Fu, Dejun Jiang, Huiyong Sun, Junmei Wang, Xujun Zhang, Gaoqi Weng, Hui Liu, Peng Tao, and Tingjun Hou*, VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations, Journal of Chemical Information and Modeling, 2021, 61, 2844-2856. [HTML]

[368].Yongchang Xu, Haiyi Chen, Huimin Zhang, Saif Ullah, Tingjun Hou*, Youjun Feng*, The MCR-3 inside linker appears as a facilitator of colistin resistance, Cell Reports, 2021, 35, 109135. [HTML]

[367]. Guoli Xiong, Zhenxing Wu, Jiacai Yi, Li Fu, Zhijiang Yang, Changyu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Aiping Lu, Xiang Chen, Tingjun Hou*, Dongsheng Cao*, ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties, Nucleic Acids Research, 2021, 49(W1), W5-W14. [HTML]

[366]. Jike Wang, Huiyong Sun, Jiawen Chen, Dejun Jiang, Zhe Wang, Zhenxing Wu, Xi Chen*, Dongsheng Cao*, Tingjun Hou*, DeepChargePredictor: A web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms, Bioinformatics, 2021, 37, 4255-4257. [HTML]

[365]. Guoli Xiong, Yue Zhao, Lu Liu, Zhongye Ma, Aiping Lu, Yan Cheng, Tingjun Hou*, Dongsheng Cao*, Computational Bioactivity Fingerprint Similarities To Navigate the Discovery of Novel Scaffolds, Journal of Medicinal Chemistry, 2021, 64, 7544-7554. [HTML]

[364]. Zhenxing Wu, Dejun Jiang, Jike Wang, Chang-Yu Hsieh*, Dongsheng Cao*, Tingjun Hou*, Mining Toxicity Information from Large Amounts of Toxicity Data, Journal of Medicinal Chemistry, 2021, 64, 6924-6936. [HTML]

[363]. Cangsong Shen, Chunyou Mao, Chanjuan Xu, Nan Jin, Huibing Zhang, Dan-Dan Shen, Qingya Shen, Xiaomei Wang, Tingjun Hou, Zhong Chen, Philippe Rondard, Jean-Philippe Pin, Yan Zhang, Jianfeng Liu, Structural basis of GABA(B) receptor-G(i) protein coupling, Nature, 2021, 594, 594-598. [HTML]

[362]. Youqian Wu, Chao Zhang, Xiaolan Liu, Zhengfu He, Bing Shan, Qingxin Zeng, Qingwei Zhao, Huaying Zhu, Hongwei Liao, Xufeng Cen, Xiaoyan Xu, Mengmeng Zhang, Tingjun Hou, Zhe Wang, Huanhuan Yan, Shuying Yang, Yaqin Sun, Yanying Chen, Ronghai Wu, Tingxue Xie, Wei Chen, Ayaz Najafov, Songmin Ying, Hongguang Xia, ARIH1 signaling promotes anti-tumor immunity by targeting PD-L1 for proteasomal degradation, Nature Communications, 2021, 12, 2346. [HTML]

[361]. Xiaochen Zhang, Chengkun Wu, Zhijiang Yang, Zhenxing Wu, Jiacai Yi, Changyu Hsieh, Tingjun Hou*, Dongsheng Cao*, MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction, Briefings in Bioinformatics, 2021, in press. [HTML]

[360]. Gaoqi Weng, Chao Shen, Dongsheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li*, Jian Wu*, Tingjun Hou*, PROTAC-DB: an online database of PROTACs, Nucleic Acids Research, 2021, 49(D1), D1381-D1387. [HTML]

[359]. Hongyan Du, Junbo Gao, Gaoqi Weng, Junjie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dongsheng Cao*, Tingjun Hou*, CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors, Nucleic Acids Research, 2021, 49(D1), D1122-D1129. [HTML]

[358]. Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li*, Dongsheng Cao*, Tingjun Hou*, Identification of Active Molecules against Mycobacterium Tuberculosis through Machine Learning, Briefings in Bioinformatics, 2021, 22, bbab068. [HTML]

[357]. Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Dongsheng Cao*, Tingjun Hou*, Hyperbolic Relational Graph Convolution Networks Plus: a Simple but Highly Efficient QSAR-modeling Method, Briefings in Bioinformatics, 2021, 22, bbab112. [HTML]

[356]. Ziyi Yang, Zhijiang Yang, Yue Zhao, Mingzhu Yin, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, PySmash: Python package and individual executable program for representative substructure generation and application, Briefings in Bioinformatics, 2021, 22, bbab017. [HTML]

[355]. Yuan Wang, ZheWang, Jiacheng Liu, Yunwen Wang, Rui Wu, Rong Sheng*, Tingjun Hou*, Discovery of novel HBV capsid assembly modulators by structure-based virtual screening and bioassays, Bioorganic & Medicinal Chemistry, 2021, 36, 116096. [HTML]

[354]. Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dongsheng Cao*, Jian Wu*, Tingjun Hou*, Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models, Journal of Cheminformatics, 2021, 13, 12. [HTML]

[353]. Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang*, Dongsheng Cao*, Tingjun Hou*, ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions, Journal of Cheminformaticse, 2021, 13, 6. [HTML]

[352]. Ziyi Yang, Zhijiang Yang, Junhong He, Aiping Lu, Shao Liu, Tingjun Hou*, Dongsheng Cao*, Benchmarking the mechanisms of frequent hitters: limitation of PAINS alerts, Drug Discovery Today, 2021, 26, 1353-1358. [HTML]

[351]. Li Fu, Ziyi Yang, Zhijiang Yang, Mingzhu Yin, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou*, Dongsheng Cao*, QSAR-assisted-MMPA to expand chemical transformation space for lead optimization, Briefings in Bioinformatics, 2021, 22, bbaa374. [HTML]

[350]. Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang, Dongsheng Cao*, Tingjun Hou*, Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?, Briefings in Bioinformatics, 2021, 22, bbaa410. [HTML]

[349]. Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dongsheng 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 in Bioinformatics, 2021, 22, bbaa321. [HTML]

[348]. Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions Briefings in Bioinformatics,2021, 22, 497-514. [HTML]

[347]. Jingyu Zhu, Kan Li, Li Yu, Yun Chen, Yanfei Cai, Jian Jin*, Tingjun Hou*, Targeting phosphatidylinositol 3‐kinase gamma (PI3Kγ): Discovery and development of its selective inhibitors, Medicinal Research Reviews, 2021, 43, 1599-1621. [HTML]

[346]. Ziyi Yang, Jie Dong, Zhijiang Yang, Mingzhu Yin, Hongli Jiang, Aiping Lu, Xiang Chen, Tingjun Hou*, Dongsheng Cao*, ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds, Briefings in Bioinformatics, 2021, 22, bbaa282. [HTML]

[345]. Jie Dong, Minfeng Zhu, Yonghuan Yun, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, BioMedR: An R/CRAN Package for Integrated Data Analysis Pipeline in Biomedical Study, Briefings in Bioinformatics, 2021, 22, 474-484. [HTML]

[344]. Ziyi Yang, Zhijiang Yang, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Scopy: an integrated negative design python library for desirable HTS/VS database design, Briefings in Bioinformatics, 2021, 22, bbaa194. [HTML]

[343]. Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dongsheng Cao*, Tingjun Hou*, Beware of the generic machine learning-based scoring functions in structure-based virtual screening, Briefings in Bioinformatics, 2021, 22, bbaa070. [HTML]

[342]. Guoli Xiong, Wenling Ye, Chao Shen, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Improving Structure-Based Virtual Screening Performance via Learning from Scoring Function Components, Briefings in Bioinformatics, 2021, 22, bbaa094. [HTML]

[341]. Jike Wang, Dongsheng Cao, Cunchen Tang, Lei Xu, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun, Tingjun Hou, DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges, Briefings in Bioinformatics, 2021, 22, bbaa183. [HTML]

Year 2020

[340]. Suqing Yang, Qing Ye, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Current Advances in Ligand-based Target Prediction, WIRES Computational Molecular Science, 2020, e1504. [HTML]

[339]. Zhiguo Wang*, Guo Li, Zhou Tian, Xiaoqin Lou, Yining Huang, Lihui Wang, Jianfeng Li*, Tingjun Hou*, and Junping Liu*, Insight Derived from Molecular Dynamics Simulation into the Selectivity Mechanism Targeting c-MYC G-Quadruplex, Journal of Physical Chemistry B, 2020, 124, 9773-9784. [HTML]

[338]. Jike Wang, Dongsheng Cao, Cunchen Tang, Xi Chen*, Huiyong Sun*, Tingjun Hou*, Fast and accurate prediction of partial charges using circular-atom-descriptor-based machine learning, Bioinformatics, 2020, 36, 4721-4728. [HTML]

[337]. Xueping Hu, Xin Chai, Xuwen Wang, Mojie Duan, Jinping Pang, Weitao Fu, Dan Li*, Tingjun Hou*, Advances in the computational development of androgen receptor antagonists, Drug Discovery Today, 2020, 25, 1453-146. [HTML]

[336]. Wenling Ye, Chao Shen, Guoli Xiong, Junjie Ding, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring, Journal of Chemical Information and Modeling, 2020, 60, 4216-4230. [HTML]

[335]. Gaoqi Weng, Junbo Gao, Zhe Wang, Ercheng Wang, Xueping Hu, Xiaojun Yao, Dongsheng Cao*, Tingjun Hou*, Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes, Journal of Chemical Theory and Computation, 2020, 16, 3959-3969. [HTML]

[334]. Yangshun Tang, Bo Feng, Yi Wang, Huiyong Sun, Yi You, Jie Yu, Bing Chen, Cengli Xu, Yeping Ruan, Sunliang Cui, Gang Hu, Tingjun Hou*, Zhong Chen*, Structure‐based discovery of caspase‐1 inhibitor with therapeutic potential for febrile seizures and later enhanced epileptogenic susceptibility, British Journal of Pharmacology, 2020, 17, 3519-3534. [HTML]

[333].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, Journal of Chemical Information and Modeling, 2020, 60, 5353-5365. [HTML]

[332]. Ziyi Yang, Jie Dong, Zhijiang Yang, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays, Journal of Chemical Information and Modeling, 2020, 60, 2031-2042. [HTML]

[331]. Qing Yu, Zhiguo Hu, Yanwen Shen, Yihang Jiang, Peichen Pan, Tingjun Hou, Zhenqiang Pan, Jing Huang, Yi Sun, Gossypol inhibits cullin neddylation by targeting SAG-CUL5 and RBX1-CUL1 complexes, Neoplasia, 2020, 22, 179-191. [HTML]

[330]. Li Fu, Lu Liu, Zhijiang Yang, Pan Li, Junjie Ding, Yonghuan Yun, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis, Journal of Chemical Information and Modeling, 2020, 60, 63-76. [HTML]

[329]. Dejun Jiang, Tailong Lei, Zhe Wang, Chao Shen, Dongsheng Cao*, Tingjun Hou*, ADMET Evaluation in Drug Discovery. 20. Prediction of Breast Cancer Resistance Protein Inhibition through Machine Learning, Journal of Cheminformatics, 2020, 12, 16. [HTML]

[328]. Qin Tang, Weitao Fu, Minkui Zhang, Ercheng Wang, Lvhu Shan, Xin Chai, Jinping Pang, Xuwen Wang, Xiaohong Xu, Lei Xu, Dan Li*, Rong Sheng*, Tingjun Hou*, Novel androgen receptor antagonist identified by structure-based virtual screening, structural optimization, and biological evaluation, European Journal of Medicinal Chemistry, 2020, 192, 112156. [HTML]

[327]. Ziyi Yang, Junhong He, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Frequent hitters: nuisance artifacts in high-throughput screening, Drug Discovery Today, 2020, 25, 657-667. [HTML]

[326]. Ziyi Yang, Junhong He, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, The Application of Negative Design to Design More Desirable Virtual Screening Library, Journal of Medicinal Chemistry, 2020, 63, 4411–4429. [HTML]

[325]. Zhe Wang, Xuwen Wang, Yu Kang, HaiYang Zhong, Chao Shen, Xiaojun Yao, Dongsheng Cao*, Tingjun Hou*, Binding Affinity and Dissociation Pathway Predictions for a Series of USP7 Inhibitors with Pyrimidinone Scaffold by Multiple Computational Methods, Physical Chemistry Chemical Physics, 2020, 22, 5487-5499. [HTML]

[324]. Zhe Wang, Huiyong Sun, Chao Shen, Xueping Hu, Junbo Gao, Dan Li, Dongsheng Cao*, Tingjun Hou*, Combined Strategies in Structure-based Virtual Screening, Physical Chemistry Chemical Physics, 2020, 22, 3149-3159. [HTML]

[323]. Chao Shen, Junjie Ding, Zhe Wang, Dongsheng Cao, Xiaoqin Ding, Tingjun Hou*, From machine learning to deep learning: advances in scoring functions for computational docking, WIRES Computational Molecular Science, 2020, 10, e1429. [HTML]

[322]. Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou*, Comprehensive assessment of nine docking programs on Type II Kinase Inhibitors: prediction accuracy of sampling power, scoring power and screening power, Briefings in Bioinformatics, 2020, 21, 282-297. [HTML]

Year 2019

[321]. Zhenxing Wu, Tailong Lei, Chao Shen, Zhe Wang, Dongsheng Cao, Tingjun Hou*, ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches, Journal of Chemical Information and Modeling, 2019, 59, 4587-4601. [HTML]

[320]. Haiyang Zhong, Zhe Wang, Xuwen Wang, Hui Liu, Dan Li, Huanxiang Liu, Xiaojun Yao* and Tingjun Hou*, Importance of crystalline water network in docking-based virtual screening: a case study of BRD4, Physical Chemistry Chemical Physics, 2019, 21, 25276-25289. [HTML]

[319]. Jie Yu, Tianli Xie, Zhe Wang, Xuwen Wang, Su Zeng, Yu Kang*, Tingjun Hou*, DNA Methyltransferases: Emerging Targets for the Discovery of Inhibitors as Potent Anticancer Drugs, Drug Discovery Today, 2019, 24, 2323-2331.. [HTML]

[318]. Ziyi Yang, Zhijiang Yang, Jie Dong, Liangliang Wang, Liuxia Zhang, Junjie Ding, Xiaoqin Ding, Aiping Lu, Tingjun Hou*, Dongsheng Cao*, Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery, Journal of Chemical Information and Modeling, 2019, 59, 3714-3726. [HTML]

[317]. Xiaotian Kong, Peichen Pan, Huiyong Sun, Hongguang Xia, Xuwen Wang, Youyong Li, Tingjun Hou*, Drug discovery targeting anaplastic lymphoma kinase (ALK), Journal of Medicinal Chemistry, 2019, 62, 10927-10954. [HTML]

[316]. Ercheng Wang, Gaoqi Weng, Huiyong Sun, Hongyan Du, Feng Zhu, Fu Chen, Zhe Wang, Tingjun Hou*, Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of Enhanced Sampling and Variable Dielectric Model on Protein-Protein Interactions, Physical Chemistry Chemical Physics, 2019, 21, 18958-18969. [HTML]

[314]. Gaoqi Weng, Ercheng Wang, Zhe Wang, Hui Liu, Feng Zhu, Dan Li, Tingjun Hou*, HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA, Nucleic Acids Research, 2019, 47, W322-W330. [HTML]

[312]. Gaoqi Weng, Ercheng Wang, Fu Chen, Huiyong Sun, Zhe Wang, Tingjun Hou*, Assessing the performance of the MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes, Physical Chemistry Chemical Physics, 2019, 21, 10135-10145. [HTML]

[311]. 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, Bioinformatics, 2019, 35, 1777–1779. [HTML]

[310]. Lei Xu, Xiaoqin Ding, Tianhu Wang, Shanzhi Mou, Huiyong Sun*, Tingjun Hou*, Voltage-gated sodium channels：structures, functions and molecular modeling, Drug Discovery Today, 2019, 24, 1389-1397. [HTML]

[309]. Tianli Xie, Jie Yu, Weitao Fu, Zhe Wang, Lei Xu, Shan Chang, Ercheng Wang, Feng Zhu, Su Zeng, Yu Kang*, Tingjun Hou*, Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study, Physical Chemistry Chemical Physics, 2019, 21, 12931-12947. [HTML]

[308]. Tingyang Wang, Ping Song, Tingting Zhong, Xianjun Wang, Xuepeng Xiang, Qian Liu, Haiyi Chen, Tian Xia, Hong Liu, Yumiao Liu, Yanshi Hu, Lei Xu, Lijun Zhu, Hongyan Qi, Jing Shen, Tingjun Hou, Riccardo Fodde, Jimin Shao, The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stem-like properties, Oncogene, 2019, 38, 4932-4947. [HTML]

[307]. Ye Jin, Mojie Duan, Xuwen Wang, Xiaotian Kong, Wenfang Zhou, Huiyong Sun, Hui Liu, Dan Li, Huidong Yu, Youyong Li*, Tingjun Hou*, Communication between the ligand-binding pocket (LBP) and the activation function-2 (AF2) domain of androgen receptor revealed by molecular dynamics simulations, Journal of Chemical Information and Modeling, 2019, 59, 842-857. [HTML]

[306]. Haiyi Chen, Weitao Fu, Zhe Wang, Xuwen Wang, Tailong Lei, Feng Zhu, Dan Li, Shan Chang, Lei Xu, Tingjun Hou*, Reliability of docking-based virtual screening for GPCR ligands with homology modeled structures: a case study of angiotensin II type I receptor, ACS Chemical Neuroscience,  2019, 10, 677–689. [HTML]

[305]. Changwei Chen, Peichen Pan, Ziyang Deng, Dahai Wang, Qifan Wu, Lei Xu, Tingjun Hou*, Sunliang Cui*, Discovery of 3, 6-diaryl-1H-pyrazolo [3, 4-b] pyridines as potent anaplastic lymphoma kinase (ALK) inhibitors, Bioorganic & Medicinal Chemistry Letters,  2019, 29, 012-916. [HTML]

[304]. Qixing Chen, Yang Yang, Jinchao Hou, Qiang Shu, Yixuan Yin, Weitao Fu, Feng Han, Tingjun Hou, Congli Zeng, Elizabeta Nemeth, Rose Linzmeier, Tomas Ganz, Xiangming Fang, Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis, Proceedings of the National Academy of Sciences,  2019, 116, 3161-3170. [HTML]

[303]. Haili Liu, Huilong Dong, Yujin Ji, Lu Wang, Tingjun Hou, Youyong Li, The adsorption, diffusion and capacity of lithium on novel boron-doped graphene nanoribbon: A density functional theory study, Applied Surface Science,  2019, 466, 737-745. [HTML]

[302]. Wenfang Zhou, Mojie Duan, Weitao Fu, Jinping Pang, Qin Tang, Huiyong Sun, Lei Xu, Shan Chang, Dan Li*, Tingjun Hou*, Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays, Genomics, Proteomics & Bioinformatics, 2019, 16, 416-427. [HTML]

Year 2018

[301]. Peichen Pan, Jiean Chen, Xijian Li, Miyang Li, Huidong Yu, Jean J Zhao, Jing Ni, Xuwen Wang, Huiyong Sun, Sheng Tian, Feng Zhu, Feng Liu, Yong Huang*, Tingjun Hou*, Structure-based Drug Design and Identification of H2O-soluble and Low Toxic Hexacyclic Camptothecin Derivatives with Improved Efficacy in both Cancer and Lethal Inflammation Models In Vivo, Journal of Medicinal Chemistry, 2018, 61,8613–8624. [HTML]

[300]. Cheng Liu, Huilong Dong, Yujin Ji, Tingjun Hou, Youyong Li, Origin of the catalytic activity of phosphorus doped MoS 2 for oxygen reduction reaction (ORR) in alkaline solution: a theoretical study, Scientific Reports, 2018, 8, 13292. [HTML]

[299]. Na Liu, Wenfang Zhou, Yue Guo, Junmei Wang, Weitao Fu, Huiyong Sun, Dan Li, Mojie Duan*, Tingjun Hou*, Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator, Journal of Chemical Information and Modeling, 2018, 58, 1652-1661. [HTML]

[298]. Fu Chen, Huiyong Sun, Junmei Wang, Feng Zhu, Hui Liu, Zhe Wang, Tailong Lei, Youyong Li, Tingjun Hou*, Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes, RNA, 2018, 24, 1183-1194. [HTML]

[297]. Yin Yu, Huiyong Sun, Tingjun Hou, Suidong Wang, Youyong Li, Fullerene derivatives act as inhibitors of leukocyte common antigen based on molecular dynamics simulations,  RSC advances, 2018, 8, 13997-14008. [HTML]

[296]. 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, Journal of Chemical Information and Modeling, 2018, 58, 1182-1193. [HTML]

[295]. Huiyong Sun, Lili Duan, Fu Chen, Hui Liu, Zhe Wang, Peichen Pan, Feng Zhu, John Z. H. Zhang, Tingjun Hou*, Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches, Phys. Chem. Chem. Phys., 2018, 20, 14450-14460. [HTML]

[294]. Zhiyu Zhang, Rong Zhang, Linlang Li, Lijun Zhu, Shiyuan Gao, Qiran Lu, Yihui Gu, Yu Zhang, Huicui Yang, Tingjun Hou, Xuechu Zhen, Long Tai Zheng, Macrophage migration inhibitory factor (MIF) inhibitor, Z-590 suppresses cartilage destruction in adjuvant-induced arthritis via inhibition of macrophage inflammatory activation, Immunopharmacology and Immunotoxicology, 2018, 40, 149-157. [HTML]

[293]. Zhe Wang, Yu Kang, Dan Li, Huiyong Sun, Xiaowu Dong, Xiaojun Yao, Lei Xu, Shan Chang, Youyong Li, Tingjun Hou*, Benchmark Study Based on 2P2IDB to Gain Insights into the Discovery of Small-Molecule PPI Inhibitors, The Journal of Physical Chemistry B, 2018, 122, 2544-2555. [HTML]

[292]. Xiaotian Kong, Huiyong Sun, Peichen Pan, Feng Zhu, Shan Chang, Lei Xu, Youyong Li, Tingjun Hou*, Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK, Physical Chemistry Chemical Physics, 2018, 20, 4851-4863. [HTML]

[291]. Yujin Ji, Mingye Yang, Haiping Lin, Tingjun Hou, Lu Wang, Youyong Li, Shuit-Tong Lee, Janus Structures of Transition Metal Dichalcogenides as the Heterojunction Photocatalysts for Water Splitting, Journal of Physical Chemistry C, 2018, 122, 3123-3129. [HTML]

[290]. Yujin Ji, Huilong Dong, Tingjun Hou, Youyong Li, Monolayer graphitic germanium carbide (g-GeC): the promising cathode catalyst for fuel cell and lithium-oxygen battery applications, Journal of Materials Chemistry A, 2018, 6, 2212-2218. [HTML]

[288]. Huilong Dong, Yujin Ji, Tingjun Hou, Youyong Li, Two-dimensional siligraphenes as cathode catalysts for nonaqueous lithium-oxygen batteries, Carbon,  2018, 126, 580-587. [HTML]

Year 2017

[287]. 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, Journal of Cheminformatics, 2017, 9, 66. [HTML]

[286]. Peichen Pan, Huidong Yu, Qinglan Liu, Xiaotian Kong, Hu Chen, Jiean Chen, Qi Liu, Dan Li, Yu Kang, Huiyong Sun, Wenfang Zhou, Sheng Tian, Sunliang Cui, Feng Zhu, Youyong Li, Yong Huang*, Tingjun Hou*, Combating drug-resistant mutants of ALK with potent and selective Type-I1/2 inhibitors by stabilizing unique DFG-shifted loop conformation, ACS Central Science, 2017, 3, 1208-1220. [HTML]

[285]. Tailong Lei, Huiyong Sun, Yu Kang, Feng Zhu. Hui Liu, Wenfang Zhou, Zhe Wang, Dan Li, Youyong Li, Tingjun Hou*, ADMET evaluation in drug discovery. 18. Reliable prediction of chemical-induced urinary tract toxicity by boosting machine learning approaches, Molecular Pharmaceutics, 2017, 14, 3935-3953. [HTML]

[284]. Tailong Lei, Fu Chen, Hui Liu, Huiyong Sun, Yu Kang, Dan Li, Youyong Li, Tingjun Hou*, ADMET evaluation in drug discovery. 17. Development of quantitative and qualitative prediction models for chemical-induced respiratory toxicity, Molecular Pharmaceutics, 2017, 14, 2407-2421. [HTML]

[283]. 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 much time-consuming approaches, Journal of Chemical Information and Modeling, 2017, 57, 1895-1906. [HTML]

[282]. Sheng Tian, Xu Wang, Linlang Li, Xiaohu Zhang, Youyong Li, Feng Zhu, Tingjun Hou*, Xuechu Zhen*, Discovery of novel and selective adenosine A2A receptor antagonists for treating parkinson's disease through comparative structure-based virtual screening, Journal of Chemical Information and Modeling, 2017, 57, 1474-1487. [HTML]

[281]. Xiaotian Kong, Huiyong Sun, Peichen Pan, Dan Li, Feng Zhu, Shan Chang, Lei Xu, Youyong Li*, and Tingjun Hou*, How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study, Scientific Reports, 2017, 7, 9088. [HTML]

[280]. Shang Li, Nana Ai, Mingyun Shen, Yuanye Dang, Cheong-Meng Chong, Peichen Pan, Yiu Wa Kwan, Shun Wan Chan, George Pak Heng Leung, Maggie Pui Man Hoi, Tingjun Hou*, Simon Ming-Yuen Lee*, Discovery of a ROCK inhibitor, FPND, which prevents cerebral hemorrhage through maintaining vascular integrity by interference with VE-cadherin, Cell Death Discovery, 2017, 3, 17051. [HTML]

[279]. Yujin Ji, Huilong Dong, Mingye Yang, Tingjun Hou, Youyong Li, Monolayer germanium monochalcogenides (GeS/GeSe) as cathode catalysts in nonaqueous Li-O2 batteries, Physical Chemistry Chemical Physics, 2017, 19, 20457 - 20462. [HTML]

[278]. Yi Yu, Huiyong Sun, Keith Gilmore, Tingjun Hou, Sui-Dong Wang, Youyong Li, Aggregated single-walled carbon nanotubes absorbs and deforms dopamine-related proteins based on molecular dynamics simulations, ACS Applied Materials & Interfaces, 2017, 9, 32452-32462. [HTML]

[277]. Zhaoran Wang, Huilong Dong, Xiaohui Yu, Yujin Ji, Tingjun Hou, Youyong Li, Two-dimensional porous polyphthalocyanine (PPc) as an efficient gas-separation membrane for ammonia synthesis, Current Applied Physics, 2017, 17, 1765-1770. [HTML]

[276]. Huilong Dong, Yujin Ji, Tingjun Hou, Youyong Li, Two-dimensional siligraphenes as cathode catalysts for nonaqueous lithium-oxygen batteries, Carbon, 2018, 126: 580-587. [HTML]

[275]. Jun Shang, Huiyong Sun, Hui Liu, Fu Chen, Sheng Tian, Peichen Pan, Dan Li, Dexin Kong*, Tingjun Hou*, Comparative analyses of structural features and scaffold diversity for purchasable compound libraries, Journal of Cheminformatics, 2017, 9, 25. [HTML]

[274]. Hui Liu, Fu Chen, Huiyong Sun, Dan Li, Tingjun Hou*, Improving the efficiency of non-equilibrium sampling in the aqueous environment via implicit-solvent simulations, Journal of Chemical Theory and Computation, 2017, 13, 1827-1836. [HTML]

[273]. Fu Chen, Huiyong Sun, Hui Liu, Dan Li, Youyong Li, Tingjun Hou*, Predicition of luciferase inhibitors by high-performance MIEC-GBDT approach based on interaction energetic patterns, Physical Chemistry Chemical Physics, 2017, 19, 10163-10176. [HTML]

[272]. Ren Kong, Lei Xu, Lianhua Piao, Dawei Zhang, Tingjun Hou and Shan Chang, Exploring the RNA‐bound and RNA‐free human argonaute-2 by molecular dynamics simulation method, Chemical Biology & Drug Design, 2017, 90, 753-763. [HTML]

[271]. Liming Li, Min Han, Xinchi Jiang, Xianzhen Yin, Fu Chen, Tianyuan Zhang, Hao Ren, Jiwen Zhang, Tingjun Hou, Zhong Chen, Hongwei Ouyang, Yasuhiko Tabata, Youqing Shen, Jianqing Gao, Peptide-tethered hydrogel scaffold promotes recovery from spinal cord transection via synergism with mesenchymal stem cells, ACS Applied Materials & Interfaces, 2017, 9, 3330-3342. [HTML]

[270]. Mingye Yang, Lu Wang, Tingjun Hou, Youyong Li, Controlling of the electronic properties of WS2 and graphene oxide heterostructures from first-principles calculations, Journal Materials Chemistry C, 2017, 5, 201-207. [HTML]

[268]. Yunxia Liu, Krisztian Palotas, Xiao Yuan, Tingjun Hou, Haiping Lin, Youyong Li, Shuit-Tong Lee, Atomistic origins of surface defects in CH3NH3PbBr3 perovskite and their electronic structures, ACS Nano, 2017, 11, 2060-2065. [HTML]

[267]. Yujin Ji, Mingye Yang, Huilong Dong, Lu Wang, Tingjun Hou, Youyong Li, Monolayer group IVAmonochalcogenides as potential and efficient catalysts for oxygen reduction reaction from the first-principles calculations, Journal of Materials Chemistry A, 2017, 5, 1743-1741. [HTML]

[266]. Huilong Dong, Lu Wang, Liujiang Zhou, Tingjun Hou, Youyong Li, Theoretical investigations on novel SiC5 siligraphene as gas sensor for air pollutants, Carbon, 2017, 113, 114-121. [HTML]

---

Year 2016

[265]. Peichen Pan, Huiyong Sun, Hui Liu, Dan Li, Wenfang Zhou, Xiaotian Kong, Youyong Li, Huidong Yu, Tingjun Hou*, In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Filtering Criteria in Selecting Virtual Screening Candidates, Scientific Reports, 2016, 6, 37628. [HTML]

[264]. Shuangquan Wang, Huiyong Sun, Hui Liu, Dan Li, Youyong Li, Tingjun Hou*, ADMET evaluation in drug discovery. 16. Predicting hERG blockers by combining multiple pharmacophores and machine learning approaches, Molecular Pharmaceutics, 2016, 13, 2855-2866. [HTML]

[262]. Fu Chen, Hui Liu, Huiyong Sun, Peichen Pan, Youyong Li, Dan Li, Tingjing Hou*, Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking, Physical Chemistry Chemical Physics, 2016, 18, 22129-22139. [HTML]

[261]. Mojie Duan, Na Liu, Wenfang Zhou, Dan Li, Minghui Yang*, Tingjun Hou*, Structural diversity of ligand-binding androgen receptors revealed by microsecond long molecular dynamics simulations and enhanced sampling,  Journal of Chemical Theory and Computation, 2016, 12, 4611-4619. [HTML]

[260]. Ji Cao, Guanyu Lin, Yanling Gong, Peichen Pan, Yaxi Ma, Ping Huang, Meidan Ying, Tingjun Hou, Qiaojun He, Bo Yang, DNA-PKcs, a Novel Functional Target of Acriflavine, Mediates Acriflacine’s p53-dependent Synergistic Anti-tumor Efficiency with Melphalan, Cancer Letters, 2016, 383, 115-124. [HTML]

[259]. Shan Chang, Dawei Zhang, Lei Xu, Hua Wan, Tingjun Hou, Ren Kong, Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods, RNA Biology, 2016, 13, 1133-1143. [HTML]

[258]. Yu Zhang, Ruinan Gu, Jia Jia, Tingjun Hou*, Longtai Zheng, Xuechu Zhen, Inhibition of Macrophage Migration Inhibitory Factor (MIF) tautomerase activity suppresses Microglia‐mediated inflmmatory responses, Clinical and Experimental Pharmacology and Physiology, 2016, 43, 1134-1144. [HTML]

[257]. Lu Wang, Huilong Dong, Zhenyu Guo*, Liling Zhang, Tingjun Hou, Youyong Li, Potential Application of Novel Boron-doped Graphene Nanoribbon as Oxygen Reduction Reaction Catalyst, Journal Physical Chemistry C, 2016, 120, 17427-17434. [HTML]

[256]. Zubin Zhang, Hongwu Mao, Xiaolin Du, Jingyu Zhu, Yujia Xu, Siyu Wang, Xin Xu, Peng Ji, Yang Yu, Biyin Cao, Kunkun Han, Tingjun Hou, Zhuan Xu, Yan Kong, Gaofeng Jiang, Xiaowen Tang, Chunhua Qiao, Xinliang Mao, A novel small molecule agent displays potent anti-myeloma activity by inhibiting the JAK2-STAT3 signaling pathway, Oncotarget, 2016, 7, 9296-9308. [HTML]

[255]. Ke Liang, Xue Chen, Zhenyu Guo, Tingjun Hou, Xiaohong Zhang, Youyong Li, Lithium intercalation and diffusion in TiO 2 nanotubes: a first-principles investigation, Physical Chemistry Chemical Physics, 2016, 18, 24370-24376. [HTML]

[253]. Lei Xu, Dan Li, Li Tao, Yanling Yang, Youyong Li, Tingjun Hou*, Binding mechanisms of 1,4-dihydropyridine derivatives to L-ytpe calcium channel Cav1.2: Molecular Modeling Study, Molecular Biosystems, 2016, 12, 376-390. [HTML]

[252]. Xiaotian Kong, Huiyong Sun, Peichen Pan, Sheng Tian, Dan Li, Youyong Li, Tingjun Hou*, Molecular Principle of Cyclin-dependent Kinases Selectivity of 4-(Thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile Derivatives Revealed by Molecular Modeling Studies, Physical Chemistry Chemical Physics, 2016, 18, 2034-2046. [HTML]

[251]. Qian Zhang, Ting Feng, Huiyong Sun, Peichen Pan, Youyong Li, Dan Li, Tingjun Hou*, Recent advances on protein-protein docking, Current Drug Targets, 2016, 17, 1586-1594. [HTML]

[250]. Tailong Lei, Dan Li, Youyong Li, Huiyong Sun, Tingjun Hou*, ADMET Evaluation in Drug Discovery. 15. Accurate Prediction of Rat Oral Acute Toxicity Using Relevance Vector Machine and Consensus Modeling, Journal of Cheminformatics, 2016, 8, 1. [HTML]

[249]. Huiyong Sun, Pengcheng Chen, Dan Li, Youyong Li, Tingjun Hou*, Directly-binding rather than induced-fit dominated binding affinity difference in (S) and (R)-crizotinib bound MTH1, Journal of Chemical Theory and Computation, 2016, 12, 851-860. [HTML]

[248]. Huiyong Sun, Peichen Pan, Sheng Tian, Lei Xu, Xiaotian Kong, Youyong Li, Dan Li, Tingjun Hou*, Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery, Scientific Reports, 2016, 6, 24817. [HTML]

[247]. Zhe Wang, Huiyong Sun, Xiaojun Yao, Dan Li, Lei Xu, Youyong Li, Sheng Tian, Tingjun Hou*, Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: prediction accuracy of sampling power and scoring power, Physical Chemistry Chemical Physics, 2016, 18, 12964-12975. [HTML]

[246]. Hui Liu, Tingjun Hou*, CaFE: a tool for binding affinity prediction using end-point free energy methods, Bioinformatics, 2016, 32, 2216-2218. [HTML]

[245]. Yujin Ji, Huilong Dong, Haiping Lin*, Liling Zhang, Tingjun Hou, Youyong Li, Heptazine-based graphitic carbon nitride as an effective hydrogen purification membrane, RSC Advances, 2016, 6, 52377-52383. [HTML]

[244]. Yunxia Liu, Yao-Jun Dong, Zeyuan Tang, Xue-Feng Wang, Lu Wang, Tingjun Hou, Haiping Lin, Youyong Li, Stable and metallic borophene nanoribbons from first-principles calculations, Journal of Materials Chemistry C, 2016, 4, 6380-6385. [HTML]

[243]. Huilong Dong, Liujiang Zhou*, Thomas Frauenheim, Tingjun Hou, Shuit-Tong Lee, Youyong Li, SiC7 siligraphene: novel donor material with extraordinary sunlight absorption, Nanoscale, 2016, 8, 6994-6999. (Highlighted by "Chemistry World"; featured as a Hot article in the online collection.) [HTML]

[242]. Xue Chen, Oleg Prezhdo, Zeyao Ma, Tingjun Hou, Zhenyu Guo, Youyong Li, Ab Initio Phonon Coupled Nonadiabatic Relaxation Dynamics of [Au25(SH)18]-Clusters, Physica Status Solidi B: Basic Solid State Physics, 2016, 11, 716-726. [HTML]

[241]. Yujin Ji, Chunmiao Du, Xiaojuan Xu, Tingjun Hou, Youyong Li, Characterizing the morphology and efficiency of polymer solar cell by experiments and simulations, Molecular Simulation, 2016, 12, 836-845. [HTML]

[240]. Bin Lin, Huilong Dong, Chunmiao Du, Tingjun Hou, Haiping Lin, Youyong Li, B40 fullerene as a highly sensitive molecular device for NH3 detection at low bias: a first-principles study, Nanotechnology, 2016, 27, 075501. [HTML]

---

Year 2015

[239]. Jingyu Zhu, Tingjun Hou*, Xinliang Mao*, Discovery of selective phosphatidylinositol 3-kinase inhibitors to treat hematological malignancies, Drug Discovery Today, 2015, 20, 988-994. [HTML]

[238]. Sheng Tian, Junmei Wang, Youyong Li, Dan Li, Lei Xu, Tingjun Hou*, The application of in silico drug-likeness predictions in pharmaceutical research, Advanced Drug Delivery Reviews, 2015, 86, 2-10. [HTML]

[237]. Junmei Wang, Tingjun Hou, Advances in computationally modeling human oral bioavailability, Advanced Drug Delivery Reviews, 2015, 86, 11-16. [HTML]

[236]. Mingyun Shen, Peichen Pan, Youyong Li, Dan Li, Huidong Yu*, Tingjun Hou*, Farnesyltransferase (FTase) and geranylgeranyltransferase I (GGTase-I): structures, mechanism, inhibitors and molecular modeling, Drug Discovery Today, 2015, 20, 267-276. [HTML]

[235]. Shuo Deng, Lu Wang, Tingjun Hou, Youyong Li, Two-Dimensional MnO2 as a Better Cathode Mateiral for Lithium Ion Batteries, Journal of Physcal Chemistry C, 2015, 119, 28783-28788. [HTML]

[234]. Peichen Pan, Sheng Tian, Huiyong Sun, Xiaotian Kong, Wenfang Zhou, Dan Li, Youyong Li, Tingjun Hou*, 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, Journal of Chemical Information and Modeling, 2015, 55, 2693-2704. [HTML]

[232]. Chunmiao Du, Yujin Ji, Junwei Xue, Tingjun Hou, Jianxin Tang, Shuit-Tong Lee, Youyong Li, Morphology and Performance of Polymer Solar Cell Characterized by DPD Simulation and Graph Theory, Scientific Reports, 2015, 5, 16854. [HTML]

[231]. Mingyun Shen, Sheng Tian, Peichen Pan, Huiyong Sun, Dan Li, Youyong Li, Hefeng Zhou, Chuwen Li, Simon Ming-Yuen Lee*, Tingjun Hou*, Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays, Scientific Reports, 2015, 5, 16749. [HTML]

[230]. Huilong Dong, Bin Lin, Keith Gilmore, Tingjun Hou, Shuit-Tong Lee, Youyong Li, Theoretical investigations on SiC 2 siligraphene as promising metal-free catalyst for oxygen reduction reaction, Journal of Power Sources, 2015, 299, 371-379. [HTML]

[229]. Yu Zhang, Lei Xu, Zhiqiang Zhang, Zhiyu Zhang, Longtai Zheng, Dan Li, Youyong Li, Feng Liu, Kunqian Yu, Tingjun Hou*, Xuechu Zhen*, Structure-activity relationships and anti-inflammatotry activities of N-carbamothioylformamide analogues as MIF tautomerase inhibitors, Journal of Chemical Information and Modeling, 2015, 55, 1994-2004. [HTML]

[228]. Yan Guan, Huiyong Sun, Peichen Pan, Youyong Li, Dan Li*, Tingjun Hou*, Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations, Molecular Biosystems, 2015, 11, 2568-2578. [HTML]

[227]. Xiaojuan Xu, Yujin Ji, Chunmiao Du, Tingjun Hou, Youyong Li, The Prediction of the morphology and PCE of Small Molecular Organic Solar Cells, RSC Advances, 2015, 5, 70939-70948. [HTML]

[226]. Mingye Yang, Lu Wang, Min Li, Tingjun Hou, Youyong Li, Structural stability and O2 dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study, AIP Advances, 2015, 5, 067136. [HTML]

[225]. Huilong Dong, Bin Lin, Keith Gilmore, Tingjun Hou, Shuit-Tong Lee, Youyong Li, B40 fullerene: an efficient material for CO2 capture, storage and separation, Current Applied Physics, 2015, 15, 1084-1089. [HTML]

[224]. Xuejie Dang, Huilong Dong, Lu Wang, Yanfei Zhao, Zhenyu Guo, Tingjun Hou, Youyong Li, Shuit-Tong Lee, Semiconducting Graphene on Silicon from First-Principle Calculations, ACS Nano, 2015, 9, 8562-8568. [HTML]

[223]. Nan Li, Richard I. Ainsworth, Bo Ding, Tingjun Hou*, and Wei Wang*, Using Hierarchical Virtual Screening to Combat Drug Resistance of the HIV-1 Protease, Journal of Chemical Information and Modeling, 2015, 55, 1400-1412. [HTML]

[221]. Huilong Dong, Zhenyu Guo, Keith Gilmore, Chunmiao Du, Tingjun Hou, Shuit-Tong Lee, Youyong Li*, Band gap modulation of Si-C binary core/shell nanowires by composition and ratio, Nanotechnology, 2015, 26, 275201. [HTML]

[220]. Huilong Dong, Tingjun Hou, Shuit-Tong Lee, Youyong Li, New Ti-decorated B40 fullerene as a promising hydrogen storage material, Scientific Reports, 2015, 5, 09952. [HTML]

[219]. Huilong Dong, Keith Gilmore, Bin Lin, Tingjun Hou, Shuit-Tong Lee, Zhenyu Guo, and Youyong Li, Adsorption of metal adatom on nanographene: Computational investigations, Carbon, 2015, 89, 249-259. [HTML]

[218]. Min Li, Lu Wang*, Ningning Yu, Xiaotian Sun, Tingjun Hou, Youyong Li, Structural stability and band gap tunability of single-side hydrogenated graphene from first principles calculations, Journal Materials Chemistry C, 2015, 3, 3645. [HTML]

[217]. Ningning Yu, Lu Wang*, Min Li , Xiaotian Sun, Tingjun Hou, Youyong Li*, Molybdenum Disulfide as a Highly Efficient Absorbent for Non-polar Gases, Physical Chemistry Chemical Physics, 2015, 17, 11700-11704. [HTML]

[216]. Xiaotian Kong, Peichen Pan, Dan Li, Sheng Tian, Youyong Li*, Tingjun Hou*, Importance of Protein Flexibility in Ranking Inhibitor Affinities: Modeling the Binding Mechanisms of Piperidine Carboxamides as Type I1/2 ALK Inhibitors, Physical Chemistry Chemical Physics, 2015, 17, 6098-6113. [HTML]

[215]. Huiyong Sun, Sheng Tian, Youyong Li, Dan Li, Peichen Pan, Tingjun Hou*, Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations, Scientific Reports, 2015, 5, 8457. [HTML]

[214]. Huali Shi#, Sheng Tian# (co-first authors), Youyong Li, Dan Li, Huidong Yu*, Xuechu Zhen*, Tingjun Hou*, Absorption, Distribution, Metabolism, Excretion, and Toxicity Evaluation in Drug Discovery. 14. Prediction of Human Pregnane X Receptor Activators by Using Naive Bayesian Classification Technique , Chemical Research in Toxicology, 2015, 28, 116-125. [HTML]

[213]. Lei Xu, Youyong Li, Dan Li, Peng Xu, Sheng Tian, Huiyong Sun, Hui Liu, Tingjun Hou*, Exploring the Binding Mechanisms of MIF to CXCR2 by Theoretical Approaches, Physical Chemistry Chemical Physics, 2015, 17, 3370-3382. [HTML]

[212]. Jingyu Zhu, Man Wang, Yu Yang, Kunkun Han, Juan Tang, Lei Xu, Zubing Zhang, Guodong Chen, Jie Li, Chunhua Qiao, Tingjun Hou*, Xinliang Mao*, A novel PI3K inhibitor identified by a virtual screen displays potent activity against multiple myeloma, Oncotarget, 2015, 5, 3836-3848. [HTML]

---

Year 2014

[211]. Jingyu Zhu, Man Wang, Biyin Cao, Tingjun Hou*, Xinliang Mao*, Targeting the Phosphatidylinositol 3-Kinase/AKT Pathway for the Treatment of Multiple Myeloma, Current Medicinal Chemistry, 2014, 21, 3173-3187. [HTML]

[210]. Yang Zhang, Mingyun Shen, Sunliang Cui*, Tingjun Hou*, Synthesis and antiproliferative evaluation of 2-hydroxylated (E)-stilbenes, Bioorganic & Medicinal Chemistry Letters, 2014, 23, 5470-5472. [HTML]

[209]. Sheng Tian#, Huiyong Sun# (co-first authors), Peichen Pan, Dan Li, Xuechu Zhen*, Youyong Li*, Tingjun Hou*, Assessing ensemble docking-based virtual screening strategy for kinase targets by considering protein flexibility, Journal of Chemical Information and Modeling, 2014, 54, 2664-2679. (One of the most read article in the last one month) [HTML]

[208]. Huiyong Sun, Tingjun Hou*, Hongyu Zhang*, Finding Chemical Drugs for Genetic Diseases, Drug Discovery Today, 2014, 19, 1836-1840. (Feature article) [HTML]

[207]. Huiyong Sun, Youyong Li, Mingyun Shen, Sheng Tian, Lei Xu, Peichen Pan, Yan Guan, Tingjun Hou*, Assessing the Performance of MM/PBSA and MM/GBSA Methods. 5. Improved Docking Performance by Using High Solute Dielectric Constant MM/GBSA and MM/PBSA Rescoring, Physical Chemistry Chemical Physics, 2014, 16, 22035-22045. [HTML]

[206]. Cheong Meng  Chong, Mingyun Shen, Zhongyan  Zhou, Peichen Pan, Puiman Hoi, Shang Li, Liang Wang, Nana Ai, Lunqing Zhang, Cheuk-Wing Li, Huidong Yu, Tingjun Hou*, Simon Mingyuen Lee*, Discovery of a benzofuran derivative (MBPTA) as a novel ROCK inhibitor in protecting against MPP+-induced oxidative stress and cell death in SH-SY5Y cells, Free Radical Biology & Medicine, 2014, 74, 283-293. [HTML]

[205]. Pengli Tan, Zhiwei Feng, Liling Zhang, Tingjun Hou, Youyong Li, The mechanism of proton translocation in respiratory complex I from molecular dynamics, Journal of Receptors and Signal Transduction, 2014, DOI:10.3109/10799893.2014.942464. [HTML]

[204]. Xiaotian Sun, Zhiwei Feng, Liling Zhang, Tingjun Hou, Youyong Li, The selective interaction between silica nanoparticles and enzymes from molecular dynamics simulations, PLoS One, 2014, 9, e107696. [HTML]

[203]. Huilong Dong, Fenglou Gu, Min Li, Bencai Lin, Zhihong Si, Tingjun Hou, Feng Yan, Shuit-Tong Lee, and Youyong Li, Improving the alkaline stability of imidazolium cations by substitution, ChemPhysChem, 2014, 15, 3006-3014. [HTML]

[202]. Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang, Tingjun Hou*, P-loop Conformation Governed Crizotinib Resistance in G2032R-mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape, PLoS Computational Biology, 2014, 10, e1003729. [HTML]

[201]. Huiyong Sun, Youyong Li, Sheng Tian, Lei Xu, Tingjun Hou*, Assessing the Performance of MM/PBSA and MM/GBSA Methods. 4. Accuracies of MM/PBSA and MM/GBSA Methodologies Evaluated by Various Simulation Protocols using PDBbind Data Set, Physical Chemistry Chemical Physics, 2014, 16, 16719-16729. [HTML]

[200]. Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou*, MORT: a powerful fundational library for computational biology and CADD, Journal of Cheminformatics, 2014, 6, 36. (One of the most read articles in the last one month) [HTML]

[199]. Juan Tang, Jingyu Zhu, Yu Yang, Zubing Zhang, Guodong Chen, Jie Li, Chunhua Qiao, Tingjun Hou*, Xinliang Mao*, A virtual screen identified C96 as a novel inhibitor of phosphatidylinositol 3-kinase that displays potent preclinical activity in multiple myeloma in vitro and in vivo, Oncotarget, 2014, 5, 3836-3848. [HTML]

[198]. Xiaotian Sun, Zhiwei Feng, Tingjun Hou, Youyong Li , The Mechanism of Graphene Oxide as an Enzyme Inhibitor from Molecular Dynamics Simulations, ACS Applied Materials & Interfaces, 2014, 6, 7153-7163. [HTML]

[197]. Zhenyu Guo, Oleg Prezhdo, Tingjun Hou, Xue Chen, Shuit-Tong Lee, Youyong Li, Fast Energy Relaxation by Trap States Decreases Electron Mobility in TiO2 Nanotubes: Time-Domain Ab Initio Analysis, Journal of Physical Chemistry Letter, 2014, 5, 1642. [HTML]

[196]. Yedong Wang, Meiyu Wang, Huixin Qi, Peichen Pan, Tingjun Hou, Jiajun Li, Guangzhao He, Hongjian Zhang, Pathway-Dependent Inhibition of Paclitaxel Hydroxylation by Kinase Inhibitors and Assessment of Drug-Drug Interaction Potentials, Drug Metabolism and Disposition, 2014, 42, 782-795. [HTML]

[195]. Xuwen Wang, Peichen Pan, Youyong Li, Dan Li, Tingjun Hou*, Insight into the prominent performance of CX-4945 derivatives: guidance for rational design of CK2 inhibitors, Molecular Biosystems, 2014, 10, 1196-1210. [HTML]

[194]. Lei Xu, Yu Zhang, Longtai Zheng, Chunhua Qiao,Youyong Li, Dan Li, Xuechu Zhen*, Tingjun Hou*, Discovery of novel inhibitors targeting macrophage migration inhibitory factor via structure-based virtual screening and bioassays, Journal of Medicinal Chemistry, 2014, 57, 3737-3745. [HTML]

[193]. Dan Li, Lei Xu, Youyong Li, Sheng Tian, Huiyong Sun, Tingjun Hou*, ADMET Evaluation in Drug Discovery. 13. Development of in silico Prediction Models for P-glycoprotein Substrates, Molecular Pharmaceutics, 2014, 11, 716-726. [HTML]

[192]. Yan Guan, Huiyong Sun, Youyong Li, Peichen Pan, Dan Li, Tingjun Hou*, The competitive binding between inhibitors and substrates of HCV NS3/4A protease: a general mechanism of drug resistance, Antiviral Research, 2014, 103, 60-70. [HTML]

[191]. Jingyu Zhu, Peichen Pan, Youyong Li, Man Wang, Dan Li, Binyin Cao, Xinliang Mao*, Tingjun Hou*, Theoretical studies on beta and delta isoform-specific binding mechanisms of phosphoinositide 3-kinase inhibitors, Molecular Biosystems, 2014, 10, 454-466. [HTML]

---

Year 2013

[190]. Peichen Pan, Mingyun Shen, Huidong Yu, Youyong Li, Dan Li, Tingjun Hou*, Advances in the development of Rho-associated protein kinase (ROCK) inhibitors, Drug Discovery Today, 2013, 18, 1323-1333. [HTML]

[189]. Lei Xu, Youyong Li, Huiyong Sun, Xuechu Zhen, Chunhua Qiao, Sheng Tian, Tingjun Hou*, Current developments of macrophage migration inhibitory factor (MIF) inhibitors, Drug Discovery Today, 2013, 18, 592-600.[HTML]

[188]. Sichao Wang, Youyong Li, Lei Xu, Dan Li, Tingjun Hou*, Recent developments in computational prediction of hERG blockage, Current Topics in Medicinal Chemistry, 2013, 13, 1317-1326. [HTML]

[187]. Biyin Cao, Jie Li, Jingyu Zhu, Mingyun Shen, Kunkun Han, Zubin Zhang, Yang Yu, Yali Wang, Depei Wu, Suning Chen, Aining Sun, Xiaowen Tang, Yun Zhao, Chunhua Qiao, Tingjun Hou, Xinliang Mao, The Antiparasitic Clioquinol Induces Apoptosis in Leukemia and Myeloma Cells by Inhibiting Histone Deacetylase Activity, Journal of Biological Chemistry, 2013, 288, 34181-34189. [HTML]

[186]. Peichen Pan, Lin Li, Youyong Li, Dan Li*, Tingjun Hou*, Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations, Antiviral Research, 2013, 100, 356-364. [HTML]

[185]. Jie Li, Biyin Cao, Shunye Zhou, Jingyu Zhu, Zubin Zhang, Tingjun Hou, Xinliang Mao, Cyproheptadine-induced myeloma cell apoptosis is associated with inhibition of the PI3K/AKT signaling, European Journal of Haematology, 2013, 91, 514-521. [HTML]

[184]. Sheng Tian, Huiyong Sun, Youyong Li, Dan Li, Tingjun Hou*, Development and evaluation of an integrated virtual screening strategy by combining molecular docking and pharmacophore searching based on multiple protein structures, Journal of Chemical Information and Modeling, 2013, 53, 2743-2756. (One of the most read articles in the last one month) [HTML]

[183]. Huilong Dong, Tingjun Hou, Xiaotian Sun, Youyong Li*, Shuit-Tong Lee, The structures and properties of Si/SiOR2R core/shell quantum dots studied by density-functional tight-binding calculations, Applied Physics Letters, 2013, 103, 123115. [HTML]

[182]. Huiyong Sun, Youyong Li*, Dan Li, Tingjun Hou*, Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches, Journal of Chemical Information and Modeling, 2013, 53, 2376-2389. (One of the most read articles in the last one month) [HTML]

[181]. Liang Wu, Tingjun Hou, Youyong Li, K. S. Chan, Shui-Tong Lee, First-Principles Study on Migration and Coalescence of Point Defects in Mono-layer Graphene, Journal Physical Chemistry C, 2013, 117, 17066-17072. [HTML]

[180]. Qian Zhang, Junmei Wang, Ginés D. Guerrero, José M. Cecilia, José M. García, Youyong Li, Horacio Pérez-Sánchez, Tingjun Hou*, Accelerated Conformational Entropy Calculations Using Graphic Processing Units, Journal of Chemical Information and Modeling, 2013, 53, 2057-2064. [HTML]

[179]. Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang, Allosite: a method for predicting allosteric sites, Bioinformatics, 2013, 29, 2357-2359. [HTML]

[177]. Sheng Tian, Youyong Li, Dan Li, Xiaojie Xu, Junmei Wang, Qian Zhang, Tingjun Hou*, Modeling compound-target interaction network of Traditional Chinese Medicines for type II diabetes mellitus: insight for polypharmacology and drug design, Journal of Chemical Information and Modeling, 2013, 53, 1787-1803. (One of the most read articles in the last one month) [HTML]

[176]. Lei Xu, Huiyong Sun, Youyong Li, Junmei Wang, Tingjun Hou*, Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models, Journal of Physical Chemistry B, 2013, 117, 8408-8421. [HTML]

[175]. Xiaohui Yu, Tingjun Hou, Youyong Li, Xuhui Sun, Shuit-Tong Lee, Effective Band Gap Reduction of Titanium Oxide Semiconductors by Codoping from First-Principles Calculations, International Journal of Quantum Chemistry, 2013, 23, 2546-2553. [HTML]

[174]. Zhiwei Feng, Tingjun Hou, Youyong Li, Transport of nucleosides in vcCNT facilitated by sodium gradients from Molecular Dynamics, Molecular Biosystems, 2013, 9, 2142-2153. [HTML]

[173]. Yanfei Zhao, Tingjun Hou, Youyong Li, K. S. Chan, Shuit-Tong Lee, Effective increasing of optical absorption of TiO2 by introducing trivalent titanium, Applied Physics Letters, 2013, 102, 171902. [HTML]

[172]. Wei Cui, Yuanhua Cheng, Lingling Geng, Densheng Liang, Tingjun Hou*, Mingjuan Ji*, Unraveling the Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling, Journal of Chemical Information and Modeling, 2013, 53, 1157-1167. (One of the most read articles in the last one month) [HTML]

[171]. Lei Xu, Youyong Li, Huiyong Sun, Dan Li, Tingjun Hou*, Structural basis of the interactions between CXCR4 and CXCL12/SDF-1 revealed by theoretical approaches, Molecular Biosystems, 2013, 9, 2107-2117. (One of the most read articles in the last one month) [HTML]

[170]. Jiangyong Gu, Qian Li, Lirong Chen, Youyong Li, Tingjun Hou, Gu Yuang, Xiaojie Xu, Platelet Aggregation Pathway Network-Based Approach for Evaluating Compounds Efficacy, Evidence-Based Complementary and Alternative Medicine, 2013, ID 425707. [HTML]

[169]. Shunye Zhou, Youyong Li, Tingjun Hou*, Feasibility of using molecular docking-based virtual screening for searching dual target kinase inhibitors, Journal of Chemical Information and Modeling, 2013, 53, 982-996. (One of the most read article in the last one month) [HTML]

[168]. Peichen Pan, Youyong Li, Huidong Yu, Tingjun Hou*, Molecular principle of topotecan resistance by topoisomerase I mutations through molecular modeling approaches, Journal of Chemical Information and Modeling, 2013, 53, 997-1006. [HTML]

[167]. Xiaohui Yu, Tingjun Hou, Xuhui Sun, Youyong Li, Atomistic structures and phase transition of In2Se3 Nanowires studied by DFT calculations and synchrotron radiation X-ray Diffraction, Solid State Communications, 2013, 162, 28-33. [HTML]

[166]. Mingyun Shen, Huidong Yu, Youyong Li, Pixu Li, Peichen Pan, Shunye Zhou, Liling Zhang, Shang Li, Simon Ming-Yuen Lee*, Tingjun Hou*, Discovery of Rho-kinase inhibitors by docking-based virtual screening, Molecular Biosystems, 2013, 9, 1511-1521. (One of the most read articles in the last one month) [HTML]

[165]. Mingyun Shen, Shunye Zhou, Youyong Li, Peichen Pan, Liling Zhang, Tingjun Hou*, Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations, Molecular Biosystems, 2013, 9, 361-374. (Hot paper recommeneded by the editor of Molecular Biosystems) [HTML]

[164]. Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou*, Drug-likeness analysis of Traditional Chinese Medicines: 2. characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from Traditional Chinese Medicines, Journal of Cheminformatics, 2013, 5, 5. (One of the most read articles in the last one month) [HTML]

[163]. Zhiwei Feng, Tingjun Hou, Youyong Li, Docking and MD study of Histamine H4R based on the crystal structure of H1R, Journal of Molecular Graphics and Modeling, 2013, 39, 1-12. [HTML]

[162]. Ming Liu, Tingjun Hou, Zhiwei Feng, Youyong Li, The flexibility of P-glycoprotein for its poly-specific drug binding from molecular dynamics, Journal of Biomolecular Structure and Dynamics, 2013, 31, 612-629. [HTML]

[161]. Chongqian Zhang, Tingjun Hou, Youyong Li, Structure-based development of antagonists for chemokine receptor CXCR4, Current Computer-aided Drug Design, 2013, 9, 60-75. [HTML]

---

Year 2012

[160]. Lei Chen, Youyong Li, Huidong Yu, Liling Zhang, Tingjun Hou*, Computational models for predicting substrates and inhibitors of P-glycoprotein, Drug Discovery Today, 2012, 17, 343-351. [HTML]

[159]. Huilong Dong, Tingjun Hou, Yaguang Zhao, Xuefeng, Youyong Li, DFT study of cobalt porphyrin complex for living radical polymerization of olefins, Computational and Theoretical Chemistry, 2012, 1001, 51-59. [HTML]

[158]. Mingyun Shen#, Sheng Tian# (#co-first authors), Youyong Li, Qian Li, Xiaojie Xu, Junmei Wang, Tingjun Hou*, Drug-likeness analysis of Traditional Chinese Medicines: 1. Property distributions of Drug-like compounds, Non-drug-like compounds and Natural compounds from Traditional Chinese Medicines, Journal of Cheminformatics, 2012, 4, 31. (One of the most read articles in the last one month) [HTML]

[157]. Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Liling Zhang, Tingjun Hou*, A rule-based algorithm for automatic bond type perception, Journal of Cheminformatics, 2012, 4, 26. (One of the most read articles in the last one month) [HTML]

[156]. Lin Li, Youyong Li, Liling Zhang, Tingjun Hou*, Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase, Journal of Chemical Information and Modeling, 2012, 52, 2715-2729. [HTML]

[155]. Zhiwei Feng, Tingjun Hou, Youyong Li, Structure-based drug design for dopamine D3 receptor, Combinatorial Chemistry & High Throughput Screening, 2012, 15, 775-791. [HTML]

[154]. Zhiwei Feng, Tingjun Hou, Youyong Li, Unidirectional peristaltic movement in multisite drug binding pocket of AcrB from molecular dynamics simulations, Molecular Biosystems, 2012, 8, 2699-2709. [HTML]

[153]. Zhiwei Feng, Tingjun Hou, Youyong Li, Concerted movement in pH-dependent gating of FocA from molecular dynamics simulations, Journal of Chemical Information and Modeling, 2012, 52, 2119-2131. [HTML]

[152]. Sheng Tian, Junmei Wang, Youyong Li, Xiaojie Xu, Tingjun Hou*, Drug-likeness analysis of Traditional Chinese Medicines: 3. prediction of drug-likeness using machine learning approaches, Molecular Pharmaceutics, 2012, 9, 2875-2886. [HTML]

[151]. Zhiwei Feng, Tingjun Hou, and Youyong Li, Selectivity and activation of dopamine D3R receptor from molecular dynamics , Journal of Molecular Modeling, 2012, 5051-5063. [HTML]

[150]. Liang Wu, Tingjun Hou, Yi Wang, Yanfei Zhao, Zhenyu Guo, Youyong Li, Shuit-Tong Lee, First-principles study of doping effect on the phase transition of zinc oxide with transition metal doped, Journal of Alloys and Compounds, 2012, 541, 250-255. [HTML]

[149]. Lei Xu, Youyong Li, Lin Li, Shunye Zhou, Tingjun Hou*, Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations, Molecular Biosystems, 2012, 8, 2260-2273. (Hot paper highlighted by Molecular Biosystems) [HTML]

[148]. Jing Zhang#, Tingjun Hou# (co-first authors), Yang Liu, Gang Chen, Xiao Yang, Jun S. Li, Wei Wang, Systematic investigation on interactions for HIV drug resistance and cross-resistance among protease inhibitors, Journal of Proteome Science and Computational Biology, 2012, 1, 1-8. [HTML]

[147]. Dongyue Cao, Junmei Wang, Rui Zhou, Youyong Li, Huidong Yu, Tingjun Hou*, ADMET evaluation in drug discovery. 11. PharmacoKinetics Knowledge Base (PKKB) - a comprehensive database of pharmacokinetic and toxic properties for drugs, Journal of Chemical Information and Modeling, 2012, 52, 1132-1137. (The most read articles in the last one month. The most read article between April and June 2012) [HTML]

[146]. Junmei Wang, Tingjun Hou, Develop and test a solvent accessible surface area-based model in conformational entropy calculations, Journal of Chemical Information and Modeling, 2012, 52, 1199-1212. [HTML]

[145]. Yinxiang Wei, YuanFang Ma, Qing Zhao, Zhiguang Ren, Yan Li, Tingjun Hou*, Hui Peng*, New use for an old drug: inhibiting ABCG2 with sorafenib, Molecular Cancer Therapeutics, 2012, 11, 1693-1702. [HTML]

[144]. Yanfei Zhao, Tingjun Hou, Liang Wu, Youyong Li, and Shuit-Tong Lee, Density functional calculations on silicon carbide nanostructures, Journal of Computational and Theoretical Nanoscience, 2012, 9, 1980-1998. [HTML]

[143]. Tingjun Hou*, Nan Li, Youyong Li, Wei Wang*, Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models, Journal of Proteome Research, 2012, 11, 2982-2995. [HTML]

[142]. Zhiwei Feng, Tingjun Hou, Youyong Li, The studies on the interactions between β2 adrenergic receptor and Gs protein by molecular dynamics simulations, Journal of Chemical Information and Modeling, 2012, 52, 1005-1014. [HTML]

[141]. Sichao Wang, Youyong Li, Junmei Wang, Lei Chen, Liling Zhang, Huidong Yu, Tingjun Hou*, ADME evaluation in drug discovery. 12. development of binary classification models for prediction of hERG potassium channel blockage, Molecular Pharmaceutics, 2012, 9, 996-1010. [HTML]

[140]. Xiaohui Yu, Tingjun Hou, Xuhui Sun, Youyong Li, The influence of defect on Mo-doped TiO2 by first principles studies, ChemPhysChem, 2012, 13, 1514-1521. [HTML]

[139]. Junwei Xue, Tingjun Hou, Youyong Li, Optimal parameters for morphology of bulk heterojunction solar cells from simulations, Applied Physics Letters, 2012, 100, 053307. [HTML]

[137]. Zheng Xu#, Tingjun Hou# (co-first author), Nan Li#, Yang Xu, Wei Wang, Proteome-wide detection of Abl1 SH3 binding peptides by integrating computational prediction and peptide microarray, Molecular & Cellular Proteomics, 2012, 11, O111.010389. [HTML]

---

Year 2011

[136]. Fangliang Gan, Binyin Cao, Depei Wu, Zixing Chen, Tingjun Hou*, Xinliang Mao*, Exploring old drugs for the treatment of hematological malignancies, Current Medicinal Chemistry, 2011, 18, 1509-1514. [HTML]

[135]. Jingyu Zhu, Junmei Wang, Youyong Li*, Tingjun Hou*, Recent developments of in silico predictions of oral bioavailability, Combinatorial Chemistry & High Throughput Screening, 2011, 14, 362-375. [HTML]

[134]. Junmei Wang, Tingjun Hou, Recent advances on aqueous solubility prediction, Combinatorial Chemistry & High Throughput Screening, 2011, 14, 328-338. [HTML]

[133]. Nan Li, Tingjun Hou, Bo Ding, Wei Wang, Characterization of PDZ domain-peptide interaction interface based on energetic patterns, Proteins: Structure, Function, and Bioinformatics, 2011, 79, 3208-3220. [HTML]

[132]. Junmei Wang*, Tingjun Hou*, Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficients, Journal of Computational Chemistry, 2011, 32, 3505-3519. [HTML]

[131]. Junmei Wang*, Tingjun Hou*, Application of molecular dynamics simulations in molecular property prediction I: density and heat of vaporization, Journal of Chemical Theory and Computation, 2011, 7, 2151-2165. [HTML]

[130]. Sheng Tian, Youyong Li, Junmei Wang, Jian Zhang*, Tingjun Hou*, ADME evaluation in drug discovery. 9. prediction of oral bioavailability in human based on molecular properties and structural fingerprints, Molecular Pharmaceutics, 2011, 8, 841-851. (One of the most read articles in the last one month) [HTML]

[129]. Tingjun Hou*, Youyong Li, Wei Wang*, Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy, Bioinformatics, 2011, 27, 1814-1821. [HTML]

[128]. Tingjun Hou*, In silico predictions of ADME/T properties: progress and challenges, Combinatorial Chemistry & High Throughput Screening, 2011, 14, 306-306. (Meet the guest editor, Professor Hou is the guest editor of the special issue for the ADME/T predictions)

[127]. Lei Chen, Youyong Li, Qin Zhao, Hui Peng*, Tingjun Hou*, ADME evaluation in drug discovery. 10. predictions of P-glycoprotein inhibitors using recursive partitioning and naïve Bayesian classification techniques, Molecular Pharmaceutics, 2011, 8, 889-900. [HTML]

[126]. Junmei Wang, Piotr Cieplak, Jie Li, Tingjun Hou, Ray Luo, and Yong Duan, Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability, Journal of Physical Chemistry B, 2011, 115, 3091-3099. [HTML]

[125]. Yi Wang, Tingjun Hou, Sheng Tian, Shui-Tong Li, Youyong Li, Influence of doping effect on zinc oxide by first principles studies, Journal of Physical Chemistry C, 2011, 115, 7706-7716. [HTML]

[124]. William A. McLaughlin, Tingjun Hou, Susan S. Taylor, Wei Wang, The identification of novel cyclic AMP-dependent protein kinase anchoring proteins using bioinformatic filters and peptide arrays, Protein Engineering Design & Selection, 2011, 24, 333-339. [HTML]

[123]. Xinliang Mao, Tingjun Hou, Biyin Cao, Wenjie Wang, Zhihua Li, Suning Chen, Min Fei, Rose Hurren, Marcela Gronda, Depei Wu, Suzzane Trudel, Aaron D chimmer, The tricyclic anti-depressant amitriptyline inhibits D-cyclin transactivation and induces myeloma cell apoptosis by inhibiting histone deacetylases:in vitro and in silico evidence, Molecular Pharmacology, 2011, 79, 672-680. [HTML]

[122]. Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*,Assessing the performance of the MM/PBSA and MM/GBSA methods: I. The accuracy of binding free energy calculations based on molecular dynamics simulations, Journal of Chemical Information and Modeling, 2011, 51, 69-82. (The most read article of JCIM in the last 12 months) [HTML]

[121]. Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*, Assessing the performance of the Molecular Mechanics/Poisson Boltzmann Surface Area and Molecular Mechanics/ Generalized Born Surface Area methods. II. the Accuracy of ranking poses generated from docking, Journal of Computational Chemistry, 2011, 32, 866-877. (Top ten most-cited paper in JCC from 2011) [HTML]

---

Year 2010

[119]. Youyong Li, Tingjun Hou*, William A. Goddard III*, Computational modeling of structure-function of G protein-coupled receptors with applications for drug design, Current Medicinal Chemistry, 2010, 17, 1167-1180. [HTML]

[118]. Yaxue Zhao, Xuefeng Lu, Chaoyie Yang, Zhimin Huang, Wei Fu, Tingjun Hou*, Jian Zhang*, Computational modeling toward understanding agonist binding on dopamine 3, Journal of Chemical Information and Modeling, 2010, 50, 1633-1643. [HTML]

[117]. Jing Zhang#, Tingjun Hou# (Co-first author), Wei Wang, Jun S. Liu, Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance, Proceedings of the National Academy of Sciences, 2010, 107, 1321-1326. (Repoted by Science Daily, UCSD News Center, The Harvard Crimson. From the Harvard Crimson: "Describing the approach of the study as “putting a story together,” Kuritzkes said it may be possible to eventually design drugs with molecular structures that accommodate those mutations.") [HTML]

[115]. Junmei Wang, Tingjun Hou, Drug and drug candidate building block analysis, Journal of Chemical Information and Modeling, 2010, 50, 55-67. (The 5th most read article of JCIM in the past 12 months) [HTML]

---

Year 2009

[114]. Tingjun Hou*, Youyong Li, Wei Zhang, Junmei Wang, Recent development of in silico predictions of intestinal absorption and bioavailability, Combinatorial Chemistry & High Throughput Screening, 2009, 12, 497-506. [HTML]

[113]. Marcia I. Dawson, Mao Ye, Xihua Cao, ... , Tingjun Hou, ... , XiaoKun Zhang, Derivation of a retinoid X receptor scaffold from peroxisome proliferator-activated receptor gamma ligand 1-Di(1H-indol-3-yl)methyl-4-trifluoromethylbenzene, CHEMMEDCHEM, 2009, 4, 1106-1119. [HTML]

[112]. Junmei Wang, Tingjun Hou, Xiaojie Xu, Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas, Journal of Chemical Information and Modeling, 2009, 49, 571-581. [HTML]

[111]. Tingjun Hou, Zheng Xu, Wei Zhang, William A. McLaughlin, David A. Case, Yang Xu, Wei Wang, Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains, Molecular & Cellular Proteomics, 2009, 8, 639-649. [HTML]

[110]. Tingjun Hou, Wei Zhang, Jiang Wang, Wei Wang, Predicting drug resistance of the HIV-1 protease using molecular interaction energy components, Proteins: Structure, Function, and Bioinformatics, 2009, 74, 837-846. [HTML]

---

Year 2008

[109]. Tingjun Hou*, Junmei Wang, Structure - ADME relationship: still a long way to go? Expert Opinion on Drug Metabolism and Toxicology, 2008, 4, 759-771. [HTML]

[108]. Tingjun Hou, Wei Zhang, David Case, Wei Wang, Characterization of domain-peptide interaction interface: A case study on the amphiphysis-1 SH3 domain, Journal of Molecular Biology, 2008, 376, 1201-1214. [HTML]

[107]. Tingjun Hou, William McLaughlin, Wei Wang, Evaluating the potency of HIV-1 protease drugs to combat resistance, Proteins: Structure, Function, and Bioinformatics, 2008, 71, 1163-1174. [HTML]

---

Year 2007

[106]. William McLaughlin, Ken Chen, Tingjun Hou, Wei Wang, On the detection of functionally coherent groups of protein domains with an extension to protein annotation, BMC Bioinformatics, 2007, 8, 390. [HTML]

[105]. Tingjun Hou*, Junmei Wang, Youyong Li, ADME evaluation in drug discovery. 8. the prediction of human intestinal absorption by a support vector machine, Journal of Chemical Information and Modeling, 2007, 47, 2408-2415. [HTML]

[104]. Tingjun Hou*, Yon Yu, Molecular dynamics and free energy studies on the wild-type and double Mutant HIV-1 protease complexed with amprenavi and two amprenavir-related inhibitors: mechanism for binding and drug resistance, Journal of Medicinal Chemistry, 2007, 50, 1177-1188. [HTML]

[103]. Tingjun Hou*, Junmei Wang, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 7. prediction of oral absorption by correlation and classification. Journal of Chemical Information and Modeling. 2007, 47, 208-218. (This paper is the 6th most assessed article of JCIM in 2007) [HTML]

[102]. Tingjun Hou*, Junmei Wang, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 6. if the oral bioavailability in human can be effectively predicted by simple molecular properties-based rules? Journal of Chemical Information and Modeling, 2007, 47, 460-463. (This paper is the 10th most assessed article of JCIM in 2007) [HTML]

[101]. Junmei Wang, Xiangqun Xie, Tingjun Hou, Xiaojie Xu, Fast approaches for molecular polarizability calculations. Journal of Physical Chemistry A, 2007, 111, 4443-4448. [HTML]

[100]. Junmei Wang, George Krudy, Tingjun Hou, George Holland, Xiaojie Xu, Development of reliable aqueous solubility models and their application in drug-like analysis. Journal of Chemical Information and Modeling. 2007, 47, 1395-1404. [HTML]

---

Year 2006

[99]. Tingjun Hou, Junmei Wang, Wei Zhang, Wei Wang, Xiaojie Xu, Recent advances in computational prediction of drug absorption and permeability in drug discovery, Current Medicinal Chemistry, 2006, 13, 2653-2667. [HTML]

[98]. Junmei Wang, Tingjun Hou, Xiaojie Xu, Recent advances in free energy calculations with a combination of molecular mechanics and continuum models, Current Computer-Aided Drug Design, 2006, 2, 287-306. [HTML]

[97]. Tingjun Hou, Ken Chen, William McLaughlin, Benzhuo Lu, Wei Wang, Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain, PLoS Computational Biology, 2006, 2, 0046-0055. (This paper was recommended by Faculty 1000, http://www.f1000biology.com/article/id/1030930/evaluation) [HTML]

[96]. Tingjun Hou, William McLaughlin, Benzhuo Lu, Ken Chen, Wei Wang, Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. Journal of Proteome Research, 2006, 5, 32-43. [HTML]

[95]. William McLaughlin, Tingjun Hou, Wei Wang, Prediction of binding sites of peptide recognition domains: an application on Grb2 and SAP SH2 domains, Journal of Molecular Biology, 2006, 357, 1322-1334. [HTML]

[94]. Aihua Wu, Qi Chen, Ke Xia, Tingjun Hou, Xinghai Shen, Hongcheng Gao, Xiaojie Xu. Investigation on photophysical properties of a substituted 3H-indole-modified β-cyclodextrin I. conformation in water and recognition mechanism as a chemosensor, Journal of Photochemistry and Photobiology A-Chemistry, 2006, 182, 174-180. [HTML]

---

Year 2005

[93]. Benzhuo Lu, Xiaolin Chen, Tingjun Hou, J. Andrew McCammon, Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals, Journal of Chemical Physics, 2005, 123, 084904. [HTML]

[92]. Wei Zhang, Tingjun Hou, Xiaojie Xu, New Born radii deriving method for generalized Born model. Journal of Chemical Informationa and Modeling, 2005, 45, 88-93. [HTML]

[91]. Tingjun Hou, Wei Zhang, Huang Qin, Xiaojie Xu, An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model, Journal of Molecular Modeling, 2005, 11, 26-40. [HTML]

---

Year 2004

[90]. Tingjun Hou, Xiaojie Xu, Recent development and application of virtual screening in drug discovery: an overview, Current Pharmaceutical Design, 2004, 10, 1011-1033. [HTML]

[89]. Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu, Some basic data structures and algorithms for chemical generic programming, Journal of Chemical Information and Computer Sciences, 2004, 44, 1571-1575. (MORT, the new version of MHTL reported in this paper, was used in AMBER10 and released in 2008) [HTML]

[88]. Tingjun Hou, Wei Zhang, Ke Xia, Xiaojie Xu, ADME evaluation in drug discovery. 5. correlation of caco-2 permeation with simple molecular properties, Journal of Chemical Information and Computer Sciences, 2004, 44, 1585-1600. (This paper is the 11th most assessed article of JCICS in 2004) [HTML]

[87]. Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu, Binding affinity of hydroxamate inhibitors of matrix metalloproteinase-2, Journal of Molecular Modeling, 2004, 10, 112-120. [HTML]

[86]. Tingjun Hou, Ke Xia, Wei Zhang, Xiaojie Xu, ADME evaluation in drug discovery. 4. prediction of aqueous solubility based on atom contribution approach, Journal of Chemical Information and Computer Sciences, 2004, 44, 266-275. (This paper is the 10th most assessed article of JCICS in 2004. The model reported in this paper was also used in the MOE molecular simulation package) [HTML]

---

Year 2003

[85]. Tingjun Hou, Lili Zhu, Lirong Chen, Xiaojie Xu, Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies, Journal of Chemical Information and Computer Sciences, 2003, 43, 273-287. [HTML]

[84]. Tingjun Hou, Xiaojie Xu, ADME evaluation in drug discovery. 2. prediction of partition coefficient by atom-additive approach based on atom-weighted solvent accessible surface areas, Journal of Chemical Information and Computer Sciences, 2003, 43, 1058-1067. [HTML]

[83]. Tingjun Hou, Xiaojie Xu, ADME evaluation in drug discovery. 3. modeling blood-brain barrier partitioning using simple molecular descriptors. Journal of Chemical Information and Computer Sciences, 2003, 43, 2137-2152. (This database reported in this paper has been used by Bio-rad's KnowItAll system, http://www.bio-rad.com) [HTML]

[82]. Wei Zhang, Tingjun Hou, Parameters for the generalized Born model consistent with RESP atomic partial charge assignment protocol, Journal of Physical Chemistry B, 2003, 107, 9071-9078. [HTML]

---

Year 2002

[81]. Tingjun Hou, Xiaojie Xu, ADME evaluation in drug discovery. 1. applications of genetic algorithms on the prediction of blood-brain partitioning of a large set of drugs from structurally derived descriptors, Journal of Molecular Modeling, 2002, 8 337-349. [HTML]

[80]. Tingjun Hou, Xiaojie Xu, Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models, Journal of Physical Chemistry B, 2002, 106, 5527-5535. [HTML]

[79]. Tingjun Hou, Xiaojie Xu, Empirical aqueous solvation models based on accessible surface areas with implicit electrostatics, Journal of Physical Chemistry B, 2002, 106, 11295-11304. [HTML]

[78]. Tingjun Hou, Xiaojie Xu, Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics, Journal of Computer-aided Molecular Design, 2002, 16, 27-41. [HTML]

[77]. Xuebin Qiao, Tingjun Hou, Wei Zhang, SenLi Guo, Xiaojie Xu, A 3D structure database of components from Chinese traditional medicinal herb, Journal of Chemical Information and Computer Sciences, 2002, 42, 481-489. [HTML]

[76]. Senli Guo, Tingjun Hou, Xiaojie Xu, Simulation of the phase behavior of the (EO)(13)( PO )(30)(EO)(13)(Pluronic L64)/water/p-xylene system using MesoDyn, Journal of Physical Chemistry B, 2002, 106, 11397-11403. [HTML]

[75]. Yanyi Huang, Tianrong Cheng, Fuyou Li, Chunhui Huang, Tingjun Hou, Anchi Yu, Xinsheng Zhao, Xiaojie Xu, Photophysical studies on the mono- and dichromophoric hemicyanine dyes I. photoelectric conversion from the dye modified ITO electrodes, Journal of Physical Chemistry B, 2002, 106, 10020-10030. [HTML]

---

Year 2001

[74]. Tingjun Hou, Xiaojie Xu, A new molecular simulation software package  Peking University Drug Design System (PKUDDS) for structure-based drug design, Journal of Molecular Graphics and Modeling, 2001, 19, 455-465. [HTML]

[73]. Tingjun Hou, Yu An, Binggen Ru, Bi Ruchang, Xiaojie Xu, Cysteine-indepent polymerization of metallothoneins in solutions and crystals, Protein Science, 2000, 9, 2302-2312. [HTML]

[72]. Tingjun Hou, Wei Zhang, Xiaojie Xu, Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear response method, Journal of Physical Chemistry B, 2001, 105, 5304-5315. [HTML]

[71]. Tingjun Hou, Xiaojie Xu, The localization and adsorption of benzene and propylene in ITQ-1 zeolite: grand canonical Monte Carlo simulations, Journal of Molecular Structure (THEO), 2001, 535, 9-23. [HTML]

[70]. Tingjun Hou, Xiaojie Xu, The absorption of a series of aromatics in ITQ-1: Grand Canonical Monte Carlo simulations, Journal of Molecular Catalysis A: Chemical, 2001, 171, 103-114. [HTML]

[69]. Tingjun Hou, Xiaojie Xu, Three-Dimension quantitative structure activity relationship analysis of some cinnamamides, Chemometrics and Intelligent Laboratory, 2001, 56, 123-132. [HTML]

[68]. Lili Zhu, Tingjun Hou, Lirong Chen, Xiaojie Xu, 3D QSAR analyses of novel tyrosine kinase phosphorylation inhibitors based on pharmacophore alignment, Journal of Chemical Information and Computer Sciences, 2001, 41, 1032-1040. [HTML]

[67]. Lili Zhu, Tingjun Hou, Xiaojie Xu, Three-dimensional quantitative structure-activity relationship study on paullones as CDKs inhibitors using CoMSIA and CoMFA, Journal of Molecular Modeling, 2001, 7, 223-230. [HTML]

---

Year 2000

[66]. Tingjun Hou, Zhengming Li, Jie Liu, Xiaojie Xu, Three-dimensional quantitative structure activity relationship analysis of the new potent sulfonaylureas using Comparative Molecular Similarity Indices Analysis (CoMSIA), Journal of Chemical Information and Computer Sciences, 2000, 40, 1002-1009. [HTML]

[65]. Tingjun Hou, Lili Zhu, Xiaojie Xu, Adsorption and diffusion of benzene in ITQ-1 type zeolite: Grand Canonical Monte Carlo and molecular dynamics simulation study, Journal of Physical Chemistry B, 2000, 104, 9356-9364. [HTML]

[64]. Tingjun Hou, Youyong Li, Ning Liao, Xiaojie Xu, Three-dimension quantitative structure-activity relationship analysis of some cinnamamides using comparative molecular similarity indices analysis (CoMSIA), Journal of Molecular Modeling, 2000, 6, 438-445. [HTML]

[63]. Youyong Li, Tingjun Hou, Kaixuan Wang, Senli Guo, The mesodyn simulation of pluronic water mixtures using the 'equivalent chain' method, Physical Chemistry Chemical Physics, 2000, 2, 2749-2753. [HTML]

---

Year 1998~1999

[62]. Tingjun Hou, Junmei Wang, Xiaojie Xu, Automatic docking of peptides and proteins by using a genetic algorithm combined with a tabu search, Protein Engineering, 1999, 12, 639-647. [HTML]

[61]. Tingjun Hou, Junmei Wang, Ning Liao, Xiaojie Xu, Applications of genetic algorithms on the structure-activity relationships analysis of some cinnamamides, Journal of Chemical information and computer sciences, 1999, 39, 775-781. [HTML]

[60]. Tingjun Hou, Junmei Wang, Xiaojie Xu, Applications of genetic algorithms on the structure-activity correlation study of a group of non-nucleoside HIV-1 inhibitors, Chemometrics and Intelligent Laboratory system, 1999, 45, 303-310. [HTML]

[59]. Jummei Wang, Tingjun Hou, Xiaojie Xu, Automatic docking of peptides and proteins by genetic algorithm, Chemometrics and Intelligent Laboratory system, 1999, 45, 281-286. [HTML]

[58]. Junmei Wang, Tingjun Hou, Lirong Chen, Xiaojie Xu, Conformational analysis of peptides using Monte Carlo simulations combined with the genetic algorithm, Chemometrics and Intelligent Laboratory system, 1999, 45, 347-351. [HTML]

[57]. Junmei Wang, Hua Zhang, Huixin He, Tingjun Hou, Xiaojie Xu, Theoretical studies on force titration of amino-group-terminated self-assembled monolayers, Journal of Molecular Structure (THEO), 1998, 451, 295-303. [HTML]

---

Other papers published on Chinese Journals

[1]~[56]