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Haifeng Chen Profile Page
Haifeng Chen
Haifeng Chen
Associate Professor


Associate Professor and Principal Investigator, Haifeng Chen, 1990-1994, Bachelor degree, Xi’an Jiaotong University. 1994-1997, Master degree, Sichuan University. 1997-2004, Assistant professor of Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences. 2000-2003,PhD degree, University of Paris 7, France. 2005 – 2006, Postdoctoral fellow, Department of Molecular Biology & Biochemistry of University of California Irvine, CA, USA. 2007 – present, Associate professor, Department of Bioinformatics and biostatistics, Shanghai Jiaotong University and Shanghai Center for Bioinformation Technology.


1. Intrinsic disorder protein or RNA folding coupled partner binding
A large number of proteins are intrinsically disordered, however, these proteins also play functional roles in binding with multiple partners. We use molecular dynamics simulation to study the folding kinetics of p53/MDM2, TIS11d/mRNA, pKID/KIX, Brinker/DNA, RNA/U1A, and LEF/DNA. The binding of partner changes the folding pathway of disordered protein or RNA. These results give an insight into the coupled mechanism of binding and folding.
2. Misfolding mechanism of amyloid fibril related to Alzheimer’s disease.
Amyloid fibrils are found in many fatal diseases, including Alzheimer’s disease, type II diabetes mellitus, and prion disease. These diseases are linked to protein misfolding. The mechanism of fibril formation is still hotly debated and remains an important open question. Our research is focus on the aggregation mechanism of short peptide with atom molecular dynamics simulation.
3. microRNA upregulation of protein translation mechanism.
MicroRNAs are endogenous 23-25 nt RNAs that play important gene-regulatory roles in posttranscriptional regulation. Small RNAs can bind with PAZ domain of argonaute 2 (AGO2) and KH domain of FXR1 during the process of translational up-regulation. However the specific recognition among dsRNA, PAZ, and KH is poorly understood. Our research in this area involves understanding microRNA upregulation protein translation by all atom molecular dynamics (MD) simulation.
4. Structure-based drug design for antitumor and anti-HIV
We have investigated the interaction mechanism of HIV reverse transcriptase inhibitors, cyclooxygenase (COX-2) inhibitors and progesterone receptor inhibitors with molecular dynamics simulation, docking and 3D-QSAR methods. These investigations could help us to design new lead compound.


1. Fang Qin, Wei Ye, Yue Chen, Xiaodong Chen, Yixue Li, Jian Zhang, H. F. Chen*. Specific Recognition between Intrinsically Disordered LEF and DNA. Phys. Chem. Chem. Phys. 14: 538-545, 2012. (IF=3.45)
2. Z. Huang, L. Zhu, Y. Cao, G. Wu, X. Liu, Y. Chen, Q. Wang, T. Shi, Y. Zhao, Y. Wang, W. Li, Y. Li, H.F. Chen*, G. Chen, Jian Zhang. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Research. 39: D663–D669, 2011 (Database issue). (IF=7.84)
3. J. Xiong, H. Wang, G. Guo, S. Wang, L. He, H. F. Chen*, J. Wu. Male Germ Cell Apoptosis and Epigenetic Histone Modification Induced by Tripterygium wilfordii Hook F. PLoS ONE 6: e20751, 2011. (IF=4.41)
4. F. Qin, Y. Jiang, Y. Chen, M. Wu, G. Yan, W. Ye, Y. X. Li, J. Zhang, H. F. Chen*. Conformational Selection or Induced Fit for Brinker and DNA Recognition. Phys. Chem. Chem. Phys. 13,1407-1412, 2011. (IF=3.45)
5. H. Zhang, F. Qin, W. Ye, Z. Li,S. Ma, Y. Xia, Y. Jiang, J. Zhu, Y. Li, J. Zhang, H. F. Chen*. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des 78:427-437, 2011. (IF=2.53)
6. Z. Li, H. Zhang, Y. Li, J. Zhang, H. F. Chen*. Drug Resistant Mechanism of Diaryltriazine Analog Inhibitors of HIV-1 Reverse Transcriptase Using Molecular Dynamics Simulation and 3D-QSAR. Chem Biol Drug Des 77:63-74, 2011. (IF=2.53)
7. F. Qin, Y. Chen, M. Wu, Y. X. Li, J. Zhang, H. F. Chen*. Induced Fit or Conformational Selection for RNA/U1A folding. RNA 16:1053-1061,2010. (IF=6.05)
8. Y. Chen, Y.J. He, M. Wu, G. Yan, Y.X. Li, J. Zhang, H. F. Chen*. Insight into the Stability of Cross-β Amyloid Fibril from Molecular Dynamics Simulation. Biopolymers 93: 578-586, 2010. (IF=2.61)
9. Y. Chen, Z. Li , H. F. Chen*. Computational Study of CCR5 Antagonist with Support Vector Machines and Three Dimensional Quantitative Structure Activity Relationship Methods. Chem Biol Drug Des 75: 295-309, 2010. (IF=2.53)
10. H. F. Chen*. Post-translational Modification of Phosphorylated KID from Molecular Dynamics Simulation. PLoS ONE 4: e6516, 2009. (IF=4.41)
11. F. Qin, Y. Chen, Y. X. Li, H. F. Chen*. Induced Fit of mRNA/TIS11d Complex. J. Chem. Phys. 131: 115103, 2009. (IF=3.05)
12. H. F. Chen*. Aggregation Mechanism Investigation of the GIFQINS cross- Amyloid Fibril. Comput. Bio. Chem. 33: 41–45, 2009. (IF=2.19)
13. H. F. Chen*. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J. Chem. Theory Comput. 4: 1360-1368, 2008. (IF=5.14)
14. H. F. Chen*. Quantitative predictions of gas chromatography retention indexes with support vector machines, radial basis neural networks and multiple linear regression. Analytica Chimica Acta 609:24-36, 2008. (IF=4.35)
15. H. F. Chen*. Computational study of histamine H3-receptor antagonist with support vector machines and three dimension quantitative structure activity relationship methods. Analytica Chimica Acta 624:203-209, 2008. (IF=4.35)
16. J. Wang, C. Tan, H. F. Chen, Ray Luo. All-Atom Computer Simulations of Amyloid Fibrils Disaggregation. Biophysics Journal. 95:5037-5047, 2008. (IF=4.39)
17. H. F. Chen.* In Silico logP Prediction for a Large Data Set with Support Vector Machines, Radial Basis Neural Networks and Multiple Linear Regression. Chem Biol Drug Des 74: 142–147, 2009. (IF=2.53)
18. H. F. Chen*. Computational Study of the Binding Mode of Epidermal Growth Factor Receptor Kinase Inhibitors. Chem. Biol. Drug Des. 71:434-446, 2008. (IF=2.53)
19. Z. Li, J. Han, H. F. Chen*. Revealing Interaction Mode between HIV-1 Reverse Transcriptase and Diaryltriazine Analog Inhibitor. Chem. Biol. Drug Des. 72:350-359, 2008. (IF=2.53)
20. H. F. Chen*, M.Y. Wu, Z. Wang, D.Q. Wei. Insight into the Metabolism Rate of Quinone Analogues from Molecular Dynamics Simulation and 3D-QSMR Methods. Chem Biol Drug Des. 70:290–301, 2007. (IF=2.53)
21. H. F. Chen, R. Luo. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 129:2930-2937, 2007. (IF=9.02)


2)主持上海市浦江人才计划 (项目编号10PJD010)