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]

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

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


Papers

2020年

[331]. 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, accepted. [HTML]

[330]. 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, in press. [HTML]

[329]. 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, 2020, in press. [HTML]

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

[327]. 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, in press. [HTML]

[326]. 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, in press. [HTML]

[325]. 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]

[324]. 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, 2020, in press. [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]

2019年

[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, accepted. [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, accepted. [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]

[315]. Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z.H. Zhang*, Tingjun Hou*, End-Point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design, Chemical Reviews, 2019, 119, 9478-9508. [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]

[313]. Dan Li, Wenfang Zhou, Jinping Pang, Qin Tang, Bingling Zhong, Chao Shen, Li Xiao, Tingjun Hou*, A magic drug target: androgen receptor, Medicinal Research Reviews, 2019, 39, 1485-1514. [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, Accepted. [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]

[298]. 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, 2017, accepted. [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, accepted. [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, accepted. [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]

[269]. Yujin Ji, Mingye Yang, Huilong Dong, Tingjun Hou, Lu Wang, Youyong Li, Two-dimensional germanium monochalcogenide photocatalyst for water splitting under ultraviolet, visible to near-infrared light, Nanoscale, 2017, accepted. (Back Cover Story) [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]

[263]. Hui Liu, Dan Li, Youyong Li, Tingjun Hou*, Atomistic molecular dynamics simulations of ATP-binding cassette transporters, WIREs Computational Molecular Science, 2016, 6, 255-265. (Inside Cover Review) [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]

[254]. Cheong-Meng Chong, Man-Teng Kou, Peichen Pan, Hefeng Zhou, Nana Ai, Chuwen Li, Hai-Jing Zhong, Chung-Hang Leung, Tingjun Hou*, Simon Ming-Yuen Lee*, Discovery of a novel ROCK2 inhibitor with anti-migration effect via docking and high-content drug screening, Molecular Biosystems, 2016, 12, 2713-2721. (Inside Cover Story) [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]

[233]. Chunmiao Du, Haiping Lin, Bin Lin, Zeyao Ma, Tingjun Hou, Jianxin Tang and Youyong Li, MoS2 supported platinum single atom and its superior catalytic activity for CO oxidation: a density functional theory study, Journal of Materials Chemistry A, 2015, 3, 23113-23119. (Back Cover Story) [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]

[222]. Xiaotian Sun, Lu Wang*, Haiping Lin, Tingjun Hou, Youyong Li, Induce Magnetism into Silicene by Embedding Transition-Metal Atoms, Applied Physics Letters, 2015, 106, 222401. (Cover Story) [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]

[178]. Mingyun Shen, Shunye Zhou, Youyong Li, Dan Li, Tingjun Hou*, Theoretical study on the interaction of pyrrolopyrimidine derivatives as LIMK2 inhibitors: insight into structure-based inhibitor design, Molecular Biosystems, 2013, 9, 2435-2446. (Inside Cover Story. Hot paper recommended by referees) [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]

[138]. Jingyu Zhu, Youyong Li, Huidong Yu, Liling Zhang, Xinliang Mao*, Tingjun Hou*, Insight into the structural requirements of narlaprevir-type inhibitors of NS3/NS4A protease based on HQSAR and molecular field analyses, Combinatorial Chemistry & High Throughput Screening, 2012, 15, 439-450. (Cover Story) [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

[120]. Youyong Li, Tingjun Hou, Computational simulation of drug delivery at molecular level, Current Medicinal Chemistry, 2010, 17, 4482-4491. (Cover Review) [HTML]

[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]

[116]. Wei Cui, Zhuo, Wei, Quan Chen, Yuanhua Chen, Lingling Geng, Jiang Zhang, Jianhua Chen*, Tingjun Hou*, Mingjuan Ji*, Structure-based design of peptides against G3BP with cytotoxicity on tumor cells, Journal of Chemical Information and Modeling, 2010, 50, 380-387. (Cover Story) [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]