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欢迎访问精准分子力场与生物信息学课题组

    精准分子力场与生物信息学课题组(Precise Force Field and Bioinformatics Laboratory)创立于2007年1月,隶属于上海交通大学微生物代谢国家重点实验室。本课题组致力于计算生物学与生物信息学等学科的方法学研究,并将其应用于探索重要疾病的发生发展的分子机制索等领域。特别是在天然无规蛋白的精准分子力场方面,分别发展了基于AMBER与CHARMM的力场参数,比如ff99IDPs, ff14IDPs, ff14IDPSFF以及CHARMM36IDPSFF等。参数发表后受到美国加州大学圣地亚哥分校美国科学院院士Andrew McCammon等国内外同行的广泛关注。

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2018 新文章接收:

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研究方向

1. 天然无规蛋白精准分子力场的研究

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。分子力场是模拟天然无规蛋白的基础。而现有的结构蛋白的分子力场不能很好模拟天然无规蛋白。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,发展了天然无规蛋白的系列精准分子力场。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。这些成果将广泛应用于研究天然无规蛋白的结构与功能关系。

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2. 天然无规蛋白折叠的分子机制

结构蛋白的序列结构功能范式已经建立并被广泛接受,而天然无规蛋白的序列无规功能范式迫切需要建立。利用我们课题组发展的精准分子力场,分别研究了c-Myb, KID以及Tau蛋白的折叠机制,为揭示天然无规蛋白的序列无规功能范式提供了很好的范例。

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3. 受体与配体的别构机制研究

受体蛋白与别构剂结合之后,构象发生变化,导致受体蛋白的发生相应的变化。受体蛋白的别构效应对生物体的正常生命活动至关重要。生物体内错综复杂的生化反应都是依靠蛋白酶的催化完成的,这些酶促反应需要互不干涉、协调有序的进行,别构剂通过别构效应在不同信号通路和生化反应间起到“调度”的作用。使受体活性增强(正调节)或使受体活性降低(负调节)。我们课题组发展了基于分子动力学模拟的动态相关网络方法分别揭示了ERG蛋白的别构自抑制效应,PKM2的协同别构效应,GPCR蛋白的协同正构效应等,为受体蛋白的精准调控奠定了基础。

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研究团队

课题组长

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陈海峰

教授
精准分子力场与生物信息学课题组
微生物代谢国家重点实验室
生物信息学与生物统计学系
中国上海市闵行区东川路800号上海交通大学生命科学技术学院4号楼223室,邮编 200240
电话:00862134204348
传真:00862134204348
邮箱:haifengchen@sjtu.edu.cn

学生

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陈岳

加入时间:2008.9
专业背景:生物技术
研究方向:分子动力学模拟,药物设计
邮箱:chenyuewillsh@icloud.com

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叶纬

加入时间:2010.9
专业背景:生物信息学
研究方向:分子力场的开发与应用,多组学数据分析
邮箱:yw20055968@126.com

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杨晶旭

加入时间:2011.9
专业背景:生物信息学
研究方向:分子动力学模拟,别构通路研究及网络分析
邮箱:yangjingxusjtu@163.com

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江诚

加入时间:2012.9
专业背景:生物技术
研究方向:核糖开关,分子调控
邮箱:jiang_cheng1990@163.com

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张金脉

加入时间:2013.9
专业背景:生物化学与分子生物学
研究方向:分子动力学模拟,基因组分析,基因编辑
邮箱:zhangjinami@sjtu.edu.cn

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徐丽诗

加入时间:2013.9
专业背景:生物信息学
研究方向:分子动力学模拟,酶进化
邮箱:laplacecat@hotmail.com

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刘灏

加入时间:2014.9
专业背景:生物信息学
研究方向:天然无规蛋白力场的开发与测试
邮箱:haoliu_sjtu@foxmail.com

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Mueed Ur Rahman

加入时间:2015.1
专业背景:生物信息学
研究方向:力场分析,药物设计
邮箱: Mueed1986@sjtu.edu.cn,findmueed@yahoo.com

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钱天乐

加入时间:2015.7
专业背景:结构生物学
研究方向:分子动力学模拟,蛋白质结构与功能
邮箱: qiantianle8881@163.com

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郭翔

加入时间:2015.9
专业背景:生物信息学
研究方向:力场测试,c-Myb的折叠机制
邮箱: df1992@sjtu.edu.cn

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李泉

加入时间:2016.6
专业背景:生物信息学
研究方向:分子动力学模拟,蛋白质别构机制研究,网络分析
邮箱: leejack@sjtu.edu.cn

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Ashfaq Ur Rehman

加入时间:2016.9
专业背景:生物化学
研究方向:别构调节机制,自抑制蛋白
邮箱:raysjtu@sjtu.edu.cn

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宋东

加入时间:2016.9
专业背景:生物信息学
研究方向:分子力场开发,计算机辅助药物设计
邮箱:dongsong@sjtu.edu.cn

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但傲欢

加入时间:2017.8
专业背景:生物化工
研究方向:力场测试,天然无规蛋白的动态模拟
邮箱:danaohuan@sjtu.edu.cn

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张阳鹏

加入时间:2017.9
专业背景:生物信息学
研究方向:分子力场开发
邮箱:zhangyp@sjtu.edu.cn

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科研成果

发表文章

1. D. Song, R. Luo, H.F. Chen*. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2017, 57:1166-1178 (Citation: 2).

2. W. Ye, T. Qian, H. Liu, R. Luo, H.F. Chen*. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J. Chem. Inf. Model. 2017, 57:1153-1165 (Citation: 1).

3. Y. Cai, H. Liu, H.F. Chen. Allosteric mechanism of quinoline inhibitors for HIV RT-associated RNase with MD simulation and dynamics fluctuation network. Chem. Biol. Drug Des. 2018, in press.

4. X. Guo, J. Han, R. Luo, H.F. Chen*. Conformation Dynamics of Intrinsically Disordered Protein c-Myb with ff99IDPs Force Field. RSC Advances. 2017, 7:29713 –29721 (Citation: 0).

5. PoH. Liu, W. Ye, H.F. Chen*. Positive Cooperative Regulation of Double Binding Sites for Human Acetylcholinesterase. Chem. Biol. Drug Des. 2017, 89:694-704 (Citation: 0).

6. 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 (Citation: 2).

7. 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 (Citation: 0).

8. J. Zhang, C. Jiang, W. Ye, R. Luo, H.F. Chen*. Allosteric Pathways in Tetrahydrofolate Sensing Riboswitch with Dynamics Correlation Network. Mol. BioSyst. 2017, 13:156 -164 (Citation: 0).

9. Y. J. Ye, L. Zhou, X. Liu, H. Liu, D. Li, M. Cao, H.F. Chen, L. Xu, J. Zhu, Y. Zhao*. A novel chemical inhibitor of ABA signaling targets all ABA receptors. Plant Physiol. 2017, 173:2356-2369. (Citation: 0).

10. M. A. Hoque, Y. Zhang, L. Chen, G. Yang, M. A. Khatun, H.F. Chen, L. Hao, Y. Feng*. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem. Biol. 2017, 12:1188–1193. (Citation: 0).

11. X. Lv, H. Liu, H.F. Chen, H. Gong*. Coupling between ATP hydrolysis and protein conformational change in maltose transporter. Proteins. 2017, 85:207-220 (Citation: 0).

12. 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 (Citation: 7).

13. 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 (Citation: 1).

14. 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 (Citation: 7).

15. M. Rahman, H. Liu, A. Wadood, H.F. Chen*. Allosteric Mechanism of Cyclopropylindolobenzazepine Inhibitors for HCV NS5B Rdrp via Dynamics Correlation Network Analysis. Mol. BioSyst. 2016, 12:3280-3293 (Citation: 0).

16. 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 (Citation: 15).

17. D. Ji, W. Ye, H.F. Chen*. Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazolebased inhibitors. Mol. BioSyst. 2015, 11: 1857-1866 (Citation: 0).

18. 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 (Citation: 2.

19. 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. (Citation: 1).

20. 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 (citation: 28).

21. 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. (Citation: 1).

22. 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 (Citation: 5).

23. 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 (Citation: 7).

24. 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 (Citation: 8).

25. S. Ma, W. Ye, D. Ji, H.F. Chen*. Insight into the Binding Mode between HIV-1 Integrase and Pyrimidone Analogue Inhibitors with MD Simulation and 3D-QSAR. Med. Chem. 2013, 9:420-433 (Citation: 0).

26. 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 (Citation: 7).

27. 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 (Citation: 5).

28. 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 (Citation: 13).

29. 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 (Citation: 0).

30. 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 Res. 2011, 39: D663-D669 (Citation: 66).

31. 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 (Citation: 18).

32. 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 (Citation: 5).

33. 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 (Citation: 11).

34. 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 (Citation: 4).

35. 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 (Citation: 32).

36. 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 (Citation: 19).

37. 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 (Citation: 6).

38. H.F. Chen*. Aggregation Mechanism Investigation of the GIFQINS cross- Amyloid Fibril. Comput. Bio. Chem. 2009, 33: 41-45 (Citation: 18).

39. 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 (Citation: 6).

40. H.F. Chen*. Post-translational Modification of Phosphorylated KID from Molecular Dynamics Simulation. PLoS ONE. 2009, 4: e6516 (Citation: 37).

41. F. Qin, Y. Chen, Y. X. Li, H.F. Chen*. Induced Fit of mRNA/TIS11d Complex. J. Chem. Phys. 2009, 131: 115103 (Citation: 23).

42. H.F. Chen*. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J. Chem. Theory Comput. 2008, 4: 1360-1368 (Citation: 29).

43. H.F. Chen*. Quantitative predictions of gas chromatography retention indexes with support vector machines, radial basis neural networks and multiple linear regression. Anal. Chim. Acta. 2008, 609:24-36 (Citation: 26).

44. H.F. Chen*. Computational study of histamine H3-receptor antagonist with support vector machines and three dimension quantitative structure activity relationship methods. Anal. Chim. Acta. 2008, 624:203-209 (Citation: 10).

45. H.F. Chen*. Computational Study of the Binding Mode of Epidermal Growth Factor Receptor Kinase Inhibitors. Chem. Biol. Drug. Des. 2008, 71:434-446 (Citation: 12).

46. 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 (Citation: 8).

47. 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 (Citation: 4).

48. H.F. Chen, R. Luo*. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129:2930-2937 (Citation: 80).

49. Z. Wang, J. Zhang, H. Li, J. Li, M. Niimi, G. Ding, H.F. Chen, J. Xu, H. Zhang, Z. Xu, Y. Dai, T. Gui, S. Li, Z. Liu, S. Wu, M. Cao, L. Zhou, X. Lu, J. Wang, J. Yang, Y. Fu, D. Yang, J. Song, T. Zhu, S. Li, B. Ning, Z. Wang, T. Koike, M. Shiomi, E. Liu, L. Chen, J. Fan, Y. E. Chen, Y. Li*. Hyperlipidemia-associated gene variations and expression patterns revealed by whole-genome and transcriptome sequencing of rabbit models. Scientific Reports. 2016, 6:26942 (Citation: 0).

50. L. Dong, Q. Tan, W. Ye, D. Liu, H.F. Chen, H. Hu, D. Wen,Y. Liu, Y. Cao, J. Kang, J. Fan, W. Guo, W. Wu*. Screening and Identifying a Novel ssDNA Aptamer against Alphafetoprotein Using CE-SELEX. Scientific Reports. 2015, 5:15552 (Citation: 5).

51. Y. Zhang,J. An,G.Y. Yang,A. Bai,B. Zheng,Z. Lou,G. Wu,W. Ye,H.F. Chen, Y. Feng*, G. Manco. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426. PLos ONE. 2015, 10:e0115130 (Citation: 2 ).

52. J. Gao,X. Luo*,Y. Li,R. Gao,H.F. Chen, D. Ji. Synthesis and Biological Evaluation of 2-oxo-pyrazine-3-carboxamide-yl Nucleoside Analogues and Their Epimers as Inhibitors of Influenza A Viruses. Chem. Biol. Drug. Des. 2015, 85:245-252 (Citation: 2).

53. H. Zhang, Z. Liu, Y. Sun, J. Zhu, S. Lu, X. Liu, Q. Huang,Y. Xie, H. Zhu, S. Dang, H.F. Chen, G. Zheng, Y. Li, Y. Kuang, J. Fei, S. Chen, Z. Chen, Z.G. Wang*. Rig-I regulates NF-κB activity through binding to Nf-κb13′-UTR mRNA. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:6459-6464 (Citation: 10).

54. H. Gu,H.F. Chen, D.Q. Wei, J.F. Wang*. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. Chinese Science Bulletin, 2010, 55:2677-2683 (Citation: 13).

55. J. Wang, C. Tan, H.F. Chen, R. Luo*. All-Atom Computer Simulations of Amyloid Fibrils Disaggregation. Biophys. J. 2008, 95:5037-5047 (Citation: 22).

56. C.F. Wang, H.Q. Zheng, H.C. Wei, R. Zhang, H.F. Chen, D.Q. Wei. Structure and vibrational frequencies of Ph3PCl2 with discrete solvent molecules and in gas phase. J. Theor. Comput. Chem. 2007, 6:511-521 (Citation: 0).

57. T. Zhang, X. C. Dong, H.F. Chen, M. B. Chen. Docking Study on the Binding Modes of Sulfonylurea Analogues to ALS/AHAS and Virtual Screen of Novel Inhibitors. Acta Chimica Sinica. 2006, 64: 899-905. .

58. H.F. Chen, B.T. Fan*, C.Y. Zhao, L. Xie, C.H. Zhao, T. Zhou, K. H. Lee, G. Allaway. Computational Studies and Drug Design for HIV-1 Reverse Transcriptase Inhibitors of 3’,4’-di-O-(S)-dicamphanoyl-(+)-cis-Khellactone (DCK) Analogs. J. Comput. Aided Mol. Des. 2005, 19:243-258 (Citation: 12)..

59. Q. Zhu, J. H.Yao, S. G. Yuan*, F. Li, H.F. Chen, W. Cai, Q. Liao. Superstructure Searching Algorithm for Generic Reaction Retrieval. J. Chem. Inf. Model. 2005, 45:1214-1222.

60. C.Y. Zhao, G. Dodin, C.S. Yuan, H.F. Chen, R.L. Zheng, Z.J. Jia, B.T. Fan*. ‘In vitro’ protection of DNA from Fenton reaction by plant polyphenol verbascoside. Biochim. Biophys. Acta. 2005, 1723:114-123 (Citation: 49).

61. B.T. Fan, H.F. Chen, H.R. Xia, M. Petitjean, S.G. Yuan, A. Panaye, J. P. Doucet*. New Strategy of Mass Spectrum Simulation Based on Reduced and Concentrated Knowledge Databases. Spectroscopy Lett. 2005, 38:145-170 (Citation: 8).

62. X.J. Yao, A. Panaye, J.P. Doucet, H.F. Chen, R.S. Zhang, B.T. Fan*, M.C. Liu, Z.D. Hu. Comparative classification study of toxicity mechanisms using support vector machines and radial basis function neural networks. Anal. Chim. Acta. 2005, 535: 259-273 (Citation: 54).

63. X.J. Yao, A. Panaye, J.P. Doucet, R.S. Zhang, H.F. Chen, M.C. Liu, Z.D. Hu, B.T. Fan*. Comparative study of QSAR/QSPR correlations using support vector machines, radial basis function neural networks, and multiple linear regression. J. Chem. Inf. Model. 2004, 44:1257-1266 (Citation: 148).

64. H.F. Chen, Q. Li, X.J. Yao, B.T. Fan*, S.G. Yuan, A. Panaye, J.P. Doucet. CoMFA/CoMSIA/HQSAR and Docking Study of the Binding Mode of Selective Cyclooxygenase (COX-2) Inhibitors. QSAR Comb. Sci. 2004, 23:36-55 (Citation: 22).

65. H.F. Chen, X.J. Yao, M. Petitjean, H.R. Xia, J.H. Yao, A. Panaye, J. P. Doucet, B.T. Fan*. Insight into the Bioactivity and Metabolism of Human Glucagon Receptor Antagonists from 3D-QSAR Analyses. QSAR Comb. Sci. 2004, 23:603-620 (Citation: 8).

66. H.F. Chen, J.H. Yao, J. Sun, Q. Li, F. Li, B.T. Fan, S.G. Yuan*. Discovery of anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening. Chinese Journal of Chemistry. 2004, 22:882-887..

67. Q. Zhu, J.H. Yao,F. Li, H.F. Chen, S.G. Yuan*. Comparison the similarity of R group. Acta Chimica Sinica. 2004, 62:1585-1589.

68. Q. Zhu, J.H. Yao,F. Li, H.F. Chen, S.G. Yuan*. The new method for the classification of reaction data and reaction knowledge. Acta Chimica Sinica. 2004, 62:112-119.

69. H.F. Chen, X.J. Yao, Q. Li, S.G. Yuan, A. Panaye, J. P. Doucet, B.T. Fan*. Comparative Study of Non Nucleoside Inhibitors with HIV-1 Reverse Transcriptase Based on 3D-QSAR and Docking. SAR and QSAR in Environ. Res. 2003, 14:455-474 (Citation: 24).

70. H.F. Chen, Q. Li, X.J. Yao, B.T. Fan*, S.G. Yuan, A. Panaye, J. P. Doucet. 3D-QSAR and Docking Study of the Binding Mode of Steroids to Progesterone Receptor in Active Site. QSAR Comb. Sci. 2003, 22:604-613 (Citation: 17).

71. H.F. Chen, X.C. Dong, B.S. Zeng, K. Gao, S.G. Yuan, A. Panaye, J. P. Doucet, B.T. Fan*. Virtual Screening and Rational Drug Design Method Using Structure Generation System Based on 3D-QSAR and Docking. SAR and QSAR in Environ. Res. 2003, 14:251-264 (Citation: 5).

72. H.F. Chen, B.T. Fan*, H.R. Xia, M. Petitjean, S.G. Yuan, A. Panaye, J. P. Doucet. MASSIS: A Mass Spectra Simulation System 1. Principal and Method. Eur. J. Mass Spectrom. 2003, 9:175-186 (Citation: 6).

73. H.F. Chen, B.T. Fan*, F. Li, M. Petitjean, H.R. Xia, S.G. Yuan, A. Panaye, J. P. Doucet. MASSIS: A Mass Spectra Simulation System 2. Procedures and Performance. Eur. J. Mass Spectrom. 2003, 9:445-457 (Citation: 3).

74. H.F. Chen, J.H. Kang, Q. Li, B. S. Zeng, X. J. Yao, B. T. Fan, S.G. Yuan*. A. Panaye, J.P. Doucet. 3D-QSAR Study on Apicidin Inhibit Histone Deacetylase. Chinese Journal of Chemistry. 2003, 21:1596-1607.

75. B.S. Hayat, H.F. Chen, S.G. Yuan, R. Wen*. 3D-QSAR Study on Diindolylmethane and Its Analogues with Comparative MolecularField Analysis (CoMFA). Chinese Journal of Chemistry. 2003, 21:20-24.

76. J.H. Kang, Y.T. Zhang, J. Chen, H.F. Chen, C. J. Lin, Q. Wang, Y.X. Ou*. Nickel-induced Histone Hypoacetylation: the Role of Reactive Oxygen Species. Toxicol Sci. 2003, 74:279-286.

77. H.F. Chen, K. Gao, B.T. Fan, S.G. Yuan*, Z.J. Jia, R.L. Zheng. A. Panaye, J.P. Doucet. Virtual Screening and Rational Design of Phenylpropanoid Glycosides Analogues Based on Molecular Docking. Acta Chimica Sinica. 2002, 60:1860-1866.

78. J.H. Yao, F. Li, S.W. Luo, S.G. Yuan, H.F. Chen, Q. Li, C.Z. Zheng. Automatic Identification of Tautomeric, Alternating and Aromatic Bonds in Chemical Structures. Acta Chimica Sinica. 2002, 60, 1291-1297.

79. H.F. Chen, Q. Li, B. S. Zeng, X.C. Dong, S.G. Yuan*, M.B. Chen, C.Z. Zheng, R.S. Sun, T.M. Cheng, Y.P. Shu, R.Q. Liu. 3D-QSAR Study on Anti-mast Cell Degranulation of Isoquinoline Compounds. Acta Chimica Sinica. 2001, 59:2143-2147.

80. H.F. Chen, X.C. Dong, Y. Gu, G.Q. Chai, S.X. Zhang, S.G. Yuan*, M.B. Chen, C.Z. Zheng. Study on Anti-Gibberella Fluorine-Containing Pesticides by 3D-QSAR. Acta Chimica Sinica. 2000, 58:1074-1078.

81. Y. Gu, X.C. Dong, H.F. Chen, M.B. Chen*, S.X. Zhang, S.G. Yuan, C.Z. Zheng. 3D-QSAR Study of Flurine-Containing Pesticides. Acta Chimica Sinica. 2000, 58:1540-1545.

82. Y. Gu, M.B. Chen*, X.C. Dong, H.F. Chen, B.S. Zeng, C.L. Feng, B.Yu, Y.Z. Hui. 3D-QSAR Studies of Saponins. Acta Chimica Sinica. 2000, 58:1534-1539.

83. H.F. Chen, J.F. Li, J.H. Yao, S.G. Yuan*, C.Z. Zheng. Automatic Generation of Virtual Bio-Active Compounds. Acta Chimica Sinica. 2000, 58:529-532.

84. H.F. Chen, Y. Gu, X.C. Dong, J.F. Li, S.X. Zhang, S.G. Yuan*, M.B. Chen, C.Z. Zheng. A New Method for De Novo Bio-Active Molecular Design. Acta Chimica Sinica. 2000, 58:1168-1172.

85. H.F. Chen, S.G. Yuan*, S.W. Luo, X.C. Dong, J.H. Yao, S. Yang, C.Z. Zheng. Design of New HIV-1 Protease Inhibitors by Pharmacophore Searching. Acta Chimica Sinica. 2000, 58:287-292.

86. S.G. Yuan*, S.W. Luo, G.Q. Chai, J.H. Yao, H.F. Chen, C.Z. Zheng. From Pharmacophore to Leads: Bioactive Compound Discovery via Computer-aided Techniques. Chinese Journal of Chemistry. 1999, 17:237-243.

87. H.F. Chen, J.H. Yao, S.G. Yuan*, J. F. Li, S. Yang, C. Z. Zheng, B. T. Fan, A. Panaye, J. P. Doucet. Conformationally Flexible Searching in 3D Structure Searching System. Comput. & Appl. Chem. 1999, 16:101-104.

88. S.G. Yuan, J. H. Yao, H.F. Chen, C.Z. Zheng. Building up General Design of 3D Structure Searching System, Comput. & Appl. Chem. 1999, 15:77-80.

89. J.H. Yao, S.G. Yuan, H.F. Chen, C.Z. Zheng, S. Yang, B.T. Fan, A. Panaye, J. P. Doucet. Structure Indexing and Matching in 3D Structure Searching System. Comput. & Appl. Chem. 1999, 16:97-100.

90. S.G. Yuan, H.F. Chen, J. Xu, W.P. Xing, J.H. Yao, C.Z. Zheng. A New Definition of Molecular Similarity Based on Semantic Relation of 3D Structures. Comput. & Appl. Chem. 1999, 16:403-410.

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