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Prediction of drug metabolism mediated by cytochromes P450 Structure-based drug design targeting Farnesoid X receptor (FXR) Molecular modeling and simulation on diseases-related proteins

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Rongwei Shi, Weihua Li, Guixia Liu, and Yun Tang. Catalytic mechanism of cytochrome P450 2D6 for 4-hydroxylation of aripiprazole: A QM/MM Study. Chin J Chem, 2013, 31, 1219-1227. Ting Shi, Yuhui Han, Weihua Li, Yanlong Zhao, Yaqin Liu, Zhimin Huang, Shaoyong Lu, and Jian Zhang. Exploring the desumoylation process of SENP1: A study combined MD simulations with QM/MM calculations on SENP1-SUMO1-RanGAP1. J Chem Inf Model, 2013, 53, 2360-2368. Yanyan Chu, Weihua Li, Jianfeng Wang, Guixia Liu, and Yun Tang. Computational insights into the binding modes of Sr-Rex with cofactor NADH/NAD + and operator DNA. J Mol Model, 2013, 19, 3143-3151. Feixiong Cheng, Weihua Li, Zengrui Wu, Xichuan Wang, Chen Zhang, Jie Li, Guixia Liu, and Yun Tang. Prediction of polypharmacological profiles of drugs by the integration of chemical, side effects and therapeutic space. J Chem Inf Model, 2013, 53, 753-762. Feixiong Cheng, Weihua Li, Xichuan Wang, Yadi Zhou, Zengrui Wu, Jie Shen, and Yun Tang. Adverse drug events: Database construction and in silico prediction. J Chem Inf Model, 2013, 53, 744-752. Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Li, Jie Shen, Philip W. Lee, and Yun Tang. Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomics-derived models (PTDMs). Mol BioSyst, 2013, 9, 1316-1325. Feixiong Cheng, Weihua Li, Guixia Liu, and Yun Tang. In Silico ADMET Prediction: recent advances, current challenges and future trends. Curr Top Med Chem, 2013, 13, 1273-1289. (Invited Review) Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, and Yun Tang. Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations. J Chem Inf Model, 2012, 52, 3043-3052. Jing Fu, Pei Si, Mingyue Zheng, Lili Chen*, Xu Shen, Yun Tang, and Weihua Li*. Discovery of new non-steroidal FXR ligands via a virtual screening workflow based on Phase shape and induced fit docking. Bioorg Med Chem Lett, 2012, 22, 6848-6853. Zhonghua Shen, Feixiong Cheng, You Xu, Jing Fu, Wen Xiao, Jie Shen, Guixia Liu, Weihua Li*, and Yun Tang*. Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations. PLoS One, 2012, 7, e33500. Jing Fu, Zhonghua Shen, Feixiong Cheng, Guixia Liu, Weihua Li*, and Yun Tang*. Progress in study of the structure, catalytic mechanism and inhibitors of aromatase. Acta Pharm Sinica (Yao Xue Xue Bao), 2012, 47, 18-28. Weihua Li, Jing Fu, Mingyue Zheng, Guixia Liu, and Yun Tang. Progress in the ligands and complex structures of farnesoid X receptor. Acta Pharm Sinica (Yao Xue Xue Bao), 2012, 47, 704-715. Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, and Yun Tang. admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model, 2012, 52, 3099-3105. Feixiong Cheng, Yadi Zhou, Weihua Li, Guixia Liu, and Yun Tang. Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One, 2012, 7, e41064. Feixiong Cheng, Yadi Zhou, Jie Li, Weihua Li, Guixia Liu, and Yun Tang. Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods. Mol BioSyst, 2012, 8, 2373-2384. Guoping Hu, Guanglin Kuang, Wen Xiao, Weihua Li, Guixia Liu, and Yun Tang. Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening. J Chem Inf Model, 2012, 52, 1103-1113. Feixiong Cheng, Yutaka Ikenaga, Yadi Zhou, Yue Yu, Weihua Li, Jie Shen, Zheng Du, Lei Chen, Congying Xu, Guixia Liu, Philip W. Lee, and Yun Tang. In Silico assessment of chemical biodegradability. J Chem Inf Model, 2012, 52, 655-669. Congying Xu, Feixiong Cheng, Lei Chen, Zheng Du, Weihua Li, Guixia Liu, Philip W. Lee, and Yun Tang. In silico prediction of chemical Ames mutagenicity. J Chem Inf Model, 2012, 52, 2840-2847. Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Weixing Zhou, Jin Huang, and Yun Tang. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol, 2012, 8, e1002503 Guanglin Kuang, Guoping Hu, Xianqiang Sun, Weihua Li, Guixia Liu, and Yun Tang. In Silico investigation of interactions between human cannabinoid receptor-1 and its antagonists. J Mol Model, 2012, 18, 3831-3845. Guoping Hu, Xi Li, Xuan Zhang, Yaozong Li, Lei Ma, Liu-Meng Yang, Guixia Liu, Weihua Li, Jin Huang, Xu Shen, Lihong Hu, Yong-Tang Zheng, and Yun Tang. Discovery of inhibitors to block interactions of HIV-1 integrase with human LEDGF/p75 via structure-based virtual screening and bioassays. J Med Chem, 2012, 55, 10108-10117.

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