Online updated Publications

Selected Publications

• Hai-Feng Yang, Xiao-Nan Zhang, Yan Li, Yong-Hong Zhang*, Qin Xu*, and Dong-Qing Wei. Theoretical Studies of Intracellular Concentration of Micro-organisms’ Metabolites. Scientific Reports 2016, 7: 9048. DOI:10.1038/s41598-017-08793-2. (Impact factor 4.3)
  
• Cheng-Dong Li, Qin Xu*, Ruo-Xu Gu, Jing Qu, Dong-Qing Wei*. The dynamic binding of cholesterol to the multiple sites of C99: as revealed by coarse-grained and all-atom simulations. Phys Chem Chem Phys. 2017 Feb 1; 19(5):3845-3856. DOI: 10.1039/c6cp07873g.(Impact factor: 4.4)
• Hui-Yuan Zhang, Qin Xu*, Yu-Kun Wang, Tang-Zhen Zhao, Dan Hu, and Dong-Qing Wei*. Passive Transmembrane Permeation Mechanisms of Monovalent Ions Explored by Molecular Dynamics Simulations. J. Chem. Theory Comput., 2016; 12 (10): 4959–4969. DOI: 10.1021/acs.jctc.6b00695.(Impact factor: 5.3)
• Hao Dai, Qin Xu*, Yi Xiong*, Weilin Liu, Dongqing Wei*. Improved Prediction of Michaelis Constants in CYP450-Mediated Reactions by Resilient Back Propagation Algorithm. Current Drug Metabolism, 2016, 17, online. DOI: 10.2174/1389200217666160513144551 (Impact factor: 3.0)
• Huai-Meng Fan, Ruo-Xu Gu, Yan-Jing Wang, Yun-Long Pi, Yong-Hong Zhang, Qin Xu*, Dong-Qing Wei*. The Destabilization of Alzheimer’s Aβ42 Protofibrils with a Novel Drug Candidate wgx-50 by Molecular Dynamics Simulations.J. Phys. Chem. B 2015; 119(34):11196-11202.DOI: 10.1021/acs.jpcb.5b03116 (Impact factor: 3.2)
• Qi Chen, Xiaolin Cheng, Dongqing Wei, Qin Xu*. Molecular Dynamics Simulation Studies of the Wild Type and E92Q/N155H Mutant of Elvitegravir-resistance HIV-1 Integrase. Interdisciplinary Sciences-Computational Life Sciences, 2015; 7(1), 36-42. DOI: 10.1007/s12539-014-0235-8 (Impact factor: 0.9)
• Qi Chen, John K. Buolamwini, Jeremy C. Smith, Aixiu Li, Qin Xu, Xiaolin Cheng*, Dongqing Wei*. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. Journal of Chemical Information and Modeling, 2013; 53(12): 3297-3307. DOI: 10.1021/ci400537n (Impact factor:  4.3)
• Ruo-Xu Gu, Limin A. Liu, Yong-Hua Wang*, Qin Xu, Dong-Qing Wei*. Structural comparison of the wild type and drug resistant mutants of the influenza M2 proton channel by molecular dynamics simulations.  J. Phys. Chem. B, 2013; 117 (20),   6042–6051. DOI:10.1021/jp312396q(Impact factor: 3.2)
• Qin Xu, Jianzhuang Yao, Alexander Wlodawer, Hong Guo*. Clarification of the Mechanism of Acylation Reaction and Origin of Substrate Specificity of the Serine-Carboxyl Peptidase Sedolisin through QM/MM Free Energy Simulations. J. Phys. Chem. B, 2011; 115(10): 2470–2476. DOI: 10.1021/jp1122294  (Impact factor: 3.2).
• Qin Xu, Liyan Li, Hong Guo*. Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations, J. Phys. Chem. B, 2010; 114(32): 10594-10600. DOI: 10.1021/jp102785s (Impact factor: 3.2).
• Qin Xu, Yu-Zhuo Chu, Hao-Bo Guo, Jeremy C. Smith, Hong Guo*. Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases. Chem-Eur. J., 2009; 15(46): 12596-12599.DOI: 10.1002/chem.200902297 (Impact factor: 5.7)
• Qin Xu, Haobo Guo, Andrey Gorin, Hong Guo*. Stabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfers. J. Phys. Chem. B, 2007; 111 (23): 6501-6506. DOI:10.1021/jp0670743 (Impact factor: 3.2)
• Qin Xu, Haobo Guo, Alexander Wlodawer, Toru Nakayama, Hong Guo*. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As. Biochem., 2007; 46 (12): 3784-3792. DOI: 10.1021/bi061737p (Impact factor: 2.9)
• Qin Xu, Haobo Guo, Alexander Wlodawer, Hong Guo*. The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity. J. Am. Chem. Soc., 2006; 128 (18): 5994 -5995. DOI: 10.1021/ja058831y (Impact factor: 13.0)
• Haobo Guo, Niny Rao, Qin Xu, Hong Guo*. Origin of Tight Binding of a Near-Perfect Transition-State Analogue by Cytidine Deaminase: Implications for Enzyme Catalysis. J. Am. Chem. Soc., 2005; 127 (9): 3191-3197. DOI: 10.1021/ja0439625 (Impact factor: 13.0)
• Dongqing Wei, Qin Xu, Tangzhen Zhao, Hao Dai. Advance in Structural Bioinformatics. Springer：Advances in Experimental Medicine and Biology 2015; 827. ISBN: 978-94-017-9244-8 (Print)  978-94-017-9245-5 (Online) DOI 10.1007/978-94-017-9245-5 (Impact factor: 2.0)