Qin Xu

Education and Research Experience

  • 2001 B.S. in Biology from Peking University
  • 2008 Ph. D in Biology from University of Tennessee, Knoxville, US
  • 2009 M. S. in Statistics (2nd degree) from University of Tennessee, Knoxville, US
  • 2010-2012 Postdoctoral Research Associate, Center of Molecular Biophysics, University of Tennessee / Oak Ridge National Lab
  • 2013- Associate Research Scientist, State Key Laboratory of Microbial Metabolism and the Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
  • 2018- Research Scientist (part-time), Institute of Materials Science and Technology, Taizhou Research Institute, Zhejiang University
  • 2019- Research Scientist (part-time), Center for Biostatistics and Data Science, Shanghai Jiao Tong University / Yale University
  • 2013- Youth Editor of SCI Journal Interdisciplinary Sciences – Computational Life Sciences, and reviewers of J. Chem. Theory Comput., Phys. Chem. Chem. Phys., Chemical Biology & Drug Design, etc

Research Interests

Computational structural biology

We study the catalytic molecular mechanism, structure-function relationship and regulations of protein macromolecules and their complexes, mainly using Molecular Simulations.

Computer-aided drug design

Combining to We predict the interactions between drugs molecules and targe proteins by computational biology, bioinformatics, and biostatistical analysis, so as to design or improve drug molecules.

Biophysics

Combining molecular simulations and mathematical analyses, we explore the features and their mechanisms of microscopic motions of water molecules, charged ions and phospholipids on the surface of proteins and in biomembrane.

Selected Publications

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    Junxi Mu#, Jiali Zhou#, Qingqiu Gong*, Qin Xu*. An Allosteric Regulation Mechanism of Arabidopsis Serine/Threonine Kinase 1 (SIK1) Through Phosphorylation. Computational and Structural Biotechnology Journal, 2022; 20: 368-379. DOI: 10.1016/j.csbj.2021.12.033 (Impact factor: 7.3)

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    Yu-Fang Zhang, Xiangeng Wang, Aman Chandra Kaushik, Yanyi Chu, Xiaoqi Shan, Ming-Zhu Zhao, Qin Xu* and Dong-Qing Wei*. SPVec: A Word2vec-inspired feature representation method for Drug-Target Interaction Prediction. Frontiers in Chemistry, 2020 Jan; 7: 895. DOI: 10.3389/fchem.2019.00895 (Impact factor: 5.2)

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    Fang Li#, Changming Chen#, Si-Ying Qu, Ming-Zhu Zhao, Xiaoling Xie, Xi Wu, Lei Li, Xuefeng Wang, Qiulan Ding, Qin Xu*, Dong-Qing Wei*, Wenman Wu*. The disulfide bond between Cys22 and Cys27 in the protease domain modulate clotting activity of coagulation factor X. Thrombosis and Haemostasis, 2019-06; 119(06): 871-881. DOI: 10.1055/s-0039-1683442 (IF 5.0, Issue Cover Image Article)

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    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 2017-08-22, 7: 9048. DOI:10.1038/s41598-017-08793-2. (IF 4.1) 

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    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. 2017-02-01; 19(5):3845-3856. DOI: 10.1039/c6cp07873g. (IF: 3.9)

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    Hui-Yuan Zhang, Qin Xu*, Yu-Kun Wang, Tang-Zhen Zhao, Dan Hu, Dong-Qing Wei*. Passive Transmembrane Permeation Mechanisms of Monovalent Ions Explored by Molecular Dynamics Simulations. J. Chem. Theory Comput., 2016-09-06; 12 (10): 4959–4969. DOI: 10.1021/acs.jctc.6b00695. (IF: 5.4) 

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    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 2015-05-21; 119(34):11196-11202. DOI: 10.1021/acs.jpcb.5b03116 (Impact factor: 3.1)

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    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., 2009-10-30; 15(46): 12596-12599. DOI: 10.1002/chem.200902297 (IF: 5.2) 

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    Qin Xu, Haobo Guo, Alexander Wlodawer, Hong Guo*. The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity. J. Am. Chem. Soc., 2006-04-18; 128 (18): 5994 -5995. DOI: 10.1021/ja058831y (IF: 14.4) 

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    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., 2005-02-05; 127 (9): 3191-3197. DOI: 10.1021/ja0439625 (IF: 14.4)

Academic Rewards

  • 2017.10 500-talented plan of Taizhou, Zhejiang 

Teaching Experiences

  • 2003-2009 Teaching assistant of University of Tennessee, Knoxville, US, involved in several courses of statistics in the Dept. of Statistics, Operations and Management Science, as well as courses of Biochemistry & molecular biology lab, Molecular modeling and bioinformatics and biophysical chemistry, etc, in the Dept. of Biochemistry, Cellular and Molecular Biology.
  • 2013- Associate research scientist of Shanghai Jiao Tong University, taught courses of Computer Aided Drug Design, Computational Biology, Structural Bioinformatics, Introduction to Bioinformatics, Introduction to Database Management Systems, etc, and workshops on computational molecular dynamics simulations.
  • 1.Joint Research Funds for Translational Medicine at Shanghai Jiao Tong University (Grant No. ZH2018ZDA06), 2019/01-2021/12, Co-PI;
  • 2.National Natural Science Foundation of China (Grant No. 61832019), Foundational theory and algorithms on computational analyses of high-throughput proteomics, 2019/01-2023/12，key participant.
  • 3.National Natural Science Foundation of China (Grant No. 31770772), Molecular Dynamic Simulations on the catalysis of the serine protease activities of coagulation factors, 2018/01-2021/12, PI.
  • 4.500-talented plan of Taizhou, Zhejiang (Grant No. 2018CLY01), 2018/08-2020/08, PI.
  • 5.The National Key Research and Development Program of China (Grant No. 2016YFA0501703) from the Ministry of Science and Technology of China, The Interfacial Features and Recognition Mechanism of Protein-Protein Interactions, 2016-2021, key participant. 
  • 6.National Natural Science Foundation of China for Young Scholars (Grant No. 31400704), Molecular Dynamic Simulations Revealing the Mechanism of the Proton and Ion Permeations through Lipid Bilayer, 2015/01-2017/12, PI. 

Selected Grants

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