陳海峰檢視原始碼討論檢視歷史
| 陳海峰 | |
|---|---|
| 出生 | 1971 年1月 |
| 國籍 | 中國 |
| 知名於 | 上海交通大學生命科學技術學院副教授。 |
| 知名作品 |
《利用分子動力學模擬研究天然無規生物大分子在配體耦合下的摺疊機理》 《利用生物信息學的方法研究microRNA上調蛋白翻譯的分子機制》 |
陳海峰[1] 1971 年1月生，1994年獲得西安交通大學理學學士，1997年獲得四川大學理學碩士學位，2003年獲得法國巴黎第七大學計算化學博士學位。2005年1月至2006年12月在美國加州大學爾灣分校從事博士後研究。2007年1月回國, 現為上海交通大學生命科學技術學院教授，博士生導師。國際SCI期刊Chem. Biol. Drug Design副主編。在天然無規蛋白的分子力場和摺疊機制等方面進行了比較深入的研究，並在JACS，PNAS，Nucleic Acids Research, RNA等學術期刊發表了90多篇SCI論文，其中本人為第一作者或通信作者的SCI文章60多篇，SCI影響因子累計超過200。申請四項專利，八項軟件著作權，獲上海市科技進步一等獎及教育部自然科學二等獎。2012年評為博士生導師。研究方向是結構生物信息學，主持國家自然科學基金，科技部973、863，上海市浦江人才，上海教委創新重點等項目，在JACS、PNAS、NAR、RNA等國際刊物發表七十多篇SCI論文，其中本人為第一作者或通訊作者的論文五十多篇。上海生物信息技術研究中心課題組長。在天然無規的生物大分子摺疊機理和抗艾滋病藥物設計等方面進行了比較深入的研究，並在JACS，Nucleic Acids Research, RNA等國際著名學術期刊發表了50多篇SCI論文，其中本人為第一作者或通信作者的SCI文章37篇，SCI影響因子累計超過130。申請四項專利，八項軟件著作權，獲上海市科技進步一等獎一項。
主講課程
生物信息學、學術倫理與學術規範
獲獎情況
1. 2003年上海市科技進步一等獎
2. 2011-2012年度獲上海交通大學優秀教師三等獎
3. 2013-2014年度獲上海交通大學燭光教師二等獎
4. 2016年首屆全國大學生生命科學創新實驗大賽指導教師三等獎
研究方向
1)利用分子動力學模擬研究天然無規生物大分子在配體耦合下的摺疊機理。
2)與老年痴呆相關的澱粉纖維蛋白錯誤摺疊的分子機理。
3)利用生物信息學的方法研究microRNA上調蛋白翻譯的分子機制。
4)計算機輔助創新藥物設計
研究成果
天然無規蛋白是一類在生理條件下沒有穩定三級結構的蛋白質。這類蛋白在真核生物蛋白質組中的含量超過40%，而且天然無規蛋白與腫瘤、心血管疾病、神經退行性疾病以及糖尿病等複雜疾病的發生髮展密切相關。與結構蛋白相比，天然無規蛋白具有構象多樣性的特點難於採用X-ray、NMR等傳統實驗方法來研究。而分子力場是模擬天然無規蛋白的基礎。因而，我們從2013年開始分別矯正了八個無規傾向性的氨基酸、二十種氨基酸、八十種氨基酸環境的CMAP參數[1-4]，發展了系列精準的天然無規蛋白的分子力場。大量的測試結果表明，新力場能重現天然無規蛋白的構象特徵，並準確預測天然無規蛋白的化學位移、J-Coupling、NOE等參數。力場參數發表之後，收到大量同行的郵件索要力場參數，其中就包括美國科學院院士Andy McCammon等。這些成果將大大地推動天然無規蛋白結構與複雜疾病關係的研究，並為靶向無規蛋白的藥物研發奠定堅實的基礎。
最近主持的科研項目
1）主持國家自然科學基金面上一項（項目編號31770771） 2）主持國家自然科學基金面上一項（項目編號30770502） 3）主持上海市浦江人才計劃 （項目編號10PJD010） 4）主持上海市自然科學基金一項（項目編號10ZR1414500） 5）主持上海市教委創新重點項目一項（項目編號12ZZ023） 6）主持國家自然科學基金面上一項（項目編號31271403）
部分代表性研究論文
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.