陈海峰查看源代码讨论查看历史
| 陈海峰 | |
|---|---|
| 出生 | 1971 年1月 |
| 国籍 | 中国 |
| 知名于 | 上海交通大学生命科学技术学院副教授。 |
| 知名作品 |
《利用分子动力学模拟研究天然无规生物大分子在配体耦合下的折叠机理》 《利用生物信息学的方法研究microRNA上调蛋白翻译的分子机制》 |
陈海峰[1] 1971 年1月生，1994年获得西安交通大学理学学士，1997年获得四川大学理学硕士学位，2003年获得法国巴黎第七大学计算化学博士学位。2005年1月至2006年12月在美国加州大学尔湾分校从事博士后研究。2007年1月回国, 现为上海交通大学生命科学技术学院教授，博士生导师。国际SCI期刊Chem. Biol. Drug Design副主编。在天然无规蛋白的分子力场和折叠机制等方面进行了比较深入的研究，并在JACS，PNAS，Nucleic Acids Research, RNA等学术期刊发表了90多篇SCI论文，其中本人为第一作者或通信作者的SCI文章60多篇，SCI影响因子累计超过200。申请四项专利，八项软件著作权，获上海市科技进步一等奖及教育部自然科学二等奖。2012年评为博士生导师。研究方向是结构生物信息学，主持国家自然科学基金，科技部973、863，上海市浦江人才，上海教委创新重点等项目，在JACS、PNAS、NAR、RNA等国际刊物发表七十多篇SCI论文，其中本人为第一作者或通讯作者的论文五十多篇。上海生物信息技术研究中心课题组长。在天然无规的生物大分子折叠机理和抗艾滋病药物设计等方面进行了比较深入的研究，并在JACS，Nucleic Acids Research, RNA等国际著名学术期刊发表了50多篇SCI论文，其中本人为第一作者或通信作者的SCI文章37篇，SCI影响因子累计超过130。申请四项专利，八项软件著作权，获上海市科技进步一等奖一项。
主讲课程
生物信息学、学术伦理与学术规范
获奖情况
1. 2003年上海市科技进步一等奖
2. 2011-2012年度获上海交通大学优秀教师三等奖
3. 2013-2014年度获上海交通大学烛光教师二等奖
4. 2016年首届全国大学生生命科学创新实验大赛指导教师三等奖
研究方向
1)利用分子动力学模拟研究天然无规生物大分子在配体耦合下的折叠机理。
2)与老年痴呆相关的淀粉纤维蛋白错误折叠的分子机理。
3)利用生物信息学的方法研究microRNA上调蛋白翻译的分子机制。
4)计算机辅助创新药物设计
研究成果
天然无规蛋白是一类在生理条件下没有稳定三级结构的蛋白质。这类蛋白在真核生物蛋白质组中的含量超过40%，而且天然无规蛋白与肿瘤、心血管疾病、神经退行性疾病以及糖尿病等复杂疾病的发生发展密切相关。与结构蛋白相比，天然无规蛋白具有构象多样性的特点难于采用X-ray、NMR等传统实验方法来研究。而分子力场是模拟天然无规蛋白的基础。因而，我们从2013年开始分别矫正了八个无规倾向性的氨基酸、二十种氨基酸、八十种氨基酸环境的CMAP参数[1-4]，发展了系列精准的天然无规蛋白的分子力场。大量的测试结果表明，新力场能重现天然无规蛋白的构象特征，并准确预测天然无规蛋白的化学位移、J-Coupling、NOE等参数。力场参数发表之后，收到大量同行的邮件索要力场参数，其中就包括美国科学院院士Andy McCammon等。这些成果将大大地推动天然无规蛋白结构与复杂疾病关系的研究，并为靶向无规蛋白的药物研发奠定坚实的基础。
最近主持的科研项目
1）主持国家自然科学基金面上一项（项目编号31770771） 2）主持国家自然科学基金面上一项（项目编号30770502） 3）主持上海市浦江人才计划 （项目编号10PJD010） 4）主持上海市自然科学基金一项（项目编号10ZR1414500） 5）主持上海市教委创新重点项目一项（项目编号12ZZ023） 6）主持国家自然科学基金面上一项（项目编号31271403）
部分代表性研究论文
1. D. Song, W. Wang, W. Ye, D. Ji, R. Luo, H.F. Chen*. ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins. Chem. Biol. Drug Des. 2017, 89:5-15.
2. T. Qian, J. Wo, Y. Zhang, Q. Song, G. Feng, R. Luo, S. Lin, G. Wu, H.F. Chen*. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Scientific Reports. 2017, 7:40254.
3. J. Zhang, C. Jiang, W. Ye, R. Luo, H.F. Chen*. Allosteric Pathways in Tetrahydrofolate Sensing Riboswitch with Dynamics Correlation Network. Molecular BioSystems. 2017, 13:156 – 164.
4. J. Zhang, H. Luo, H. Liu, W. Ye, R. Luo, H.F. Chen*. Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Scientific Reports. 2016, 6: 24587.
5. W. Wang, C. Jiang, J. Zhang, W. Ye, R. Luo, H.F. Chen*. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Scientific Reports. 2016, 6: 31005.
6. J. Yang, H. Liu, X. Liu, C. Gu, R. Luo, H.F. Chen*. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J. Chem. Inf. Model. 2016, 56: 1184-1192.
7. M. Rahman, H. Liu, A. Wadood, H.F. Chen*. Allosteric Mechanism of Cyclopropylindolobenzazepine Inhibitors for HCV NS5B Rdrp via Dynamics Correlation Network Analysis. Molecular BioSystems. 2016, 12:3280-3293.
8. W. Ye, D. Ji, W. Wang, R. Luo, H.F. Chen*. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2015, 55, 1021−1029.
9. D. Ji, W. Ye, H.F. Chen*. Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazolebased inhibitors Molecular BioSystems. 2015, 11, 1857-1866.
10. L. Xu, W. Ye, C. Jiang, J. Yang, J. Zhang, Y. Feng, R. Luo, H.F. Chen*. Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis. J. Phys. Chem. B 2015, 119, 2844−2856.
11. K. Wu, J. Pang, D. Song, Y. Zhu, C. Wu, T. Shao, H.F. Chen*. Selectivity Mechanism of ATP-Competitive Inhibitors for PKB and PKA. Chem. Biol. Drug Des. 2015, 86:9-18.
12. W. Wang, W. Ye, C. Jiang, R. Luo, H.F. Chen*. New force field on modeling intrinsically disordered proteins. Chem. Biol. Drug Des. 2014, 84: 253-269.
13. Q. Yu, W. Ye, C. Jiang, R. Luo, H.F. Chen*. Specific Recognition Mechanism between RNA and KH3 Domain of Nova-2 Protein. J. Phys. Chem. B. 2014. 118, 12426−12434.
14. Q. Yu, W. Ye, W. Wang, H.F. Chen*. Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP. PLoS ONE. 2013, 8:e59627.
15. W. Wang, W. Ye, Q. Yu, C. Jiang, J. Zhang, R. Luo, H.F. Chen*.Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. J. Phys. Chem. B, 2013, 117:4912-4923.
16. W. Ye, J. Yang, Q. Yu, W. Wang, J. Hancy，R. Luo, H.F. Chen*. Kink Turn sRNA Folding upon L7Ae Binding with Molecular Dynamics Simulation. Phys. Chem. Chem. Phys., 2013, 15:18510-18522.
17. S. Ma, W. Ye, D. Ji, H.F. Chen*. Insight into the Binding Mode between HIV-1 Integrase and Pyrimidone AnalogueInhibitors with MD Simulation and 3D-QSAR. Med. Chem. 2013, 9:420-433.
18. W. Ye, F. Qin, J. Zhang, R. Luo, H.F. Chen*. Atomistic Mechanism of microRNA Translation Upregulation via Molecular Dynamics Simulations. PLoS ONE. 2012, 7: e43788.
19. W. Ye, Y. Chen, W. Wang, Q. Yu, Y. Li, J. Zhang, H.F. Chen*. Insight into the Stability of cross-beta Amyloid Fibril from VEALYL Short Peptide with Molecular Dynamics Simulation. PLoS ONE. 2012, 7: e36382.
20. F. Qin, W. Ye, Y. Chen, X. Chen, Y. Li, J. Zhang, H.F. Chen*. Specific Recognition between Intrinsically Disordered LEF and DNA. Phys. Chem. Chem. Phys. 2012, 14: 538-545.
21. G. Yan, Y. Chen, Y. Li, H.F. Chen*. Revealing Interaction Mode between HIV-1 Protease and Mannitol Analog Inhibitor. Chem. Biol. Drug Des. 2012, 79:916-925.
22. 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*, J. Zhang*. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Research. 2011, 39: D663–D669.
23. 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. 2011, 13:1407-1412.
24. 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. 2011, 78:427-437.
25. 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 2011, 6: e20751.
26. 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. 2011, 77:63-74.
27. F. Qin, Y. Chen, M. Wu, Y. X. Li, J. Zhang, H.F. Chen*. Induced Fit or Conformational Selection for RNA/U1A folding. RNA 2010, 16:1053-1061.
28. 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 2010, 93: 578-586.
29. 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 2010, 75: 295-309.
30. H.F. Chen*. Aggregation Mechanism Investigation of the GIFQINS cross-b Amyloid Fibril. Comput. Bio. Chem. 2009, 33: 41–45.
31. 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. 2009, 74: 142–147.
32. H.F. Chen*. Post-translational Modification of Phosphorylated KID from Molecular Dynamics Simulation. PLoS ONE 2009, 4: e6516.
33. F. Qin, Y. Chen, Y. X. Li, H.F. Chen*. Induced Fit of mRNA/TIS11d Complex. J. Chem. Phys. 2009, 131: 115103.
34. H.F. Chen*. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J. Chem. Theory Comput. 2008, 4: 1360-1368.
35. 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 2008, 609:24-36.
36. 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 2008, 624:203-209.
37. H.F. Chen*. Computational Study of the Binding Mode of Epidermal Growth Factor Receptor Kinase Inhibitors. Chem. Biol. Drug Des. 2008, 71:434-446.
38. Z. Li, J. Han, H.F. Chen*. Revealing Interaction Mode between HIV-1 Reverse Transcriptase and Diaryltriazine Analog Inhibitor. Chem. Biol. Drug Des. 2008, 72:350-359.
39. 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. 2007, 70:290–301.
40. H.F. Chen, R. Luo*. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129:2930-2937.