黃牛博士

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科學研究

黃牛實驗室開發基于物理學原理的計算化學理論和分子模擬技術，來研究在分子識別過程（蛋白－蛋白，蛋白－核酸和蛋白－配體相互作用）中的自由能和空間構象的變化，從而指導蛋白質結構和功能的改造，以及加速新藥的設計與開發。

黃牛博士

北京生命科學研究所高級研究員

Niu Huang, Ph.D. Associate Investigator, NIBS, Beijing, China

Phone：010-80726688-8570

Fax： 010-80726689

E-mail：huangniu@nibs.ac.cn

研究概述：

近年來，生物學領域的研究進展極大地加深了我們對和疾病密切相關的分子靶標的認識。然而，如何有效地利用這些生物學信息，進而針對疾病靶標來設計治療性藥物，還需要我們從原子水平上來掌握生物大分子的三維結構和生物功能之間的關系。我們將進一步開發基于物理學原理的計算化學理論和分子模擬技術，來研究在分子識別過程（蛋白－蛋白，蛋白－核酸和蛋白－配體相互作用）中的自由能和空間構象的變化，從而指導蛋白質結構和功能的改造，以及加速新藥的設計與開發。我們將充分利用本實驗室在大分子模擬和小分子設計方面的條件和經驗，積極促進物理和計算科學在生物學中的應用，同時探索高性能科學計算（High-performance Computing, HPC）的方法學研究。

http://www.huanglab.org.cn

主要研究方向

一．改進分子對接技術和提高打分函數的精度

在已知受體結構和作用位點的情況下，分子對接技術（Molecular Docking）可被用于自動匹配受體結合腔穴和數據庫中的小分子化合物，并預測與受體結合作用最強的一組化合物，來進行活性測試以節省新型先導化合物開發的周期和成本。我們將系統地研究和改進目前計算受體和配體結合自由能方法中的局限性因素，例如誘導契合、去溶劑化效應、熵效應，以及靜電作用的精確計算等，來提高虛擬篩選的成功率。

二．研究可被配體調控的蛋白－蛋白相互作用

蛋白－蛋白相互作用（Protein-Protein Interactions, PPIs）在許多生物學過程中起關鍵性作用。然而，基于這類重要分子靶標開發小分子藥物的成功率非常低。我們認為其中的一個重要原因是PPIs的成藥性（Druggability）與其結構的內在柔性密切相關，因此我們將利用多種構象搜尋手段來模擬PPIs界面的動態構象變化以及相關的自由能變化，預測可能的小分子結合腔穴，并且定量分析和評估這些結合位點的成藥性，從而為下一步的虛擬篩選奠定基礎。

Research Description:

The opening of the 21st century has marked with the sequencing of the human genome. Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. State-of-the-art computational chemistry and molecular modeling techniques can be applied to study a wide range of chemical and biological systems of interest, which enable us to acquire information not obtainable by experimental techniques, to investigate structural phenomena at the atomic level and to identify novel compounds with desired biological characteristics. Our laboratory is interested in developing and applying computational techniques to study the structural and energetic basis of molecular recognition (i.e., protein-protein, protein-DNA and protein-ligand interactions). Aside from its fundamental biological interest, such theoretical studies have tremendous practical values of which one of the most important is structure-based drug design.

Publications

1. Su Y, Luo Y, Zhang P, Lin H, Pu W, Zhang H, Wang H, Hao Y, Xiao Y, Zhang X, Wei X, Nie S, Zhang K, Fu Q, Chen H, Huang N, Ren Y, Wu M, Chow BKC, Chen X, Jin W, Wang F, Zhao L, Rao F. Glucose-induced CRL4^COP1-p53 axis amplifies glycometabolism to drive tumorigenesis. Mol Cell. 2023 Jul 6;83(13):2316-2331.e7.

2. Wang Q, Meng F, Xie Y, Wang W, Meng Y, Li L, Liu T, Qi J, Ni X, Zheng S, Huang J*, Huang N*. In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. ACS Cent Sci. 2023 Feb 8;9(2):252-265.

3. Zhu H, Zhang Y, Li W, Huang N*. A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years. Int J Mol Sci. 2022 Dec 15;23(24):15961.

4. Xu K, Zhang J, Duan X*, Wan X*, Huang N*, Schmidt B, Liu W*, Yang G. Redesigning and Optimizing UCSF DOCK3. 7 on Sunway TaihuLight. IEEE Transactions on Parallel and Distributed Systems 2022 33(12), 4458-4471.

5. Zhu H, Yang J*, Huang N*. Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening. J Chem Inf Model. 2022 62(22):5485-5502.

6. Li G, Cheng Y, Han C, Song C, Huang N*, Du Y*. Pyrazole-containing pharmaceuticals: target, pharmacological activity, and their SAR studies. RSC Med Chem. 2022 13(11):1300-1321.

7. Xu M, Shen C, Yang J, Wang Q, Huang N. Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening. ACS Omega. 2022 7(43):39417-39428.

8. Xu J, Shen C, Xie Y, Qiu B, Ren X, Zhou Y, Li G*, Zheng G*, Huang N*. Design, synthesis, and bioactivity evaluation of macrocyclic benzo[b]pyrido[4,3-e][1,4]oxazine derivatives as novel Pim-1 kinase inhibitors. Bioorg Med Chem Lett. 2022 Jun 30;72:128874.

9. Li L, Liao H, Meng Y, Li W, Han P, Liu K, Wang Q, Li D, Zhang Y, Wang L, Fan Z, Zhang Y, Wang Q, Zhao X*, Sun Y*, Huang N*, Qi J, Gao GF*. Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell. 2022 Aug 4;185(16):2952-2960.

10. Teng X, Chen S, Wang Q, Chen Z, Wang X, Huang N, Zheng S. Structural insights into G protein activation by D1 dopamine receptor. Sci Adv. 2022 Jun 10;8(23):eabo4158.

11. Wang JH, Tang YL, Gong Z, Jain R, Xiao F, Zhou Y, Tan D, Li Q, Huang N, Liu SQ, Ye K, Tang C, Dong MQ, Lei X. Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers. Nat Commun. 2022 Mar 18;13(1):1468.

12. Chen J, Liu N, Huang Y, Wang Y, Sun Y, Wu Q, Li D, Gao S, Wang HW*, Huang N*, Qi X*, Wang X*. Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun. 2021 Oct 27;12(1):6204.

13. Han P, Su C, Zhang Y, Bai C, Zheng A, Qiao C, Wang Q, Niu S, Chen Q, Zhang Y, Li W, Liao H, Li J, Zhang Z, Cho H, Yang M, Rong X, Hu Y, Huang N, Yan J, Wang Q, Zhao X, Gao GF, Qi J. Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun. 2021 Oct 20;12(1):6103.

14. Wang Q, Zhou Y, Huang J, Huang N. Structure, Function, and Pharmaceutical Ligands of 5-Hydroxytryptamine 2B Receptor. Pharmaceuticals (Basel). 2021 Jan 20;14(2):76.

15. Li G, Zhang W, Xie Y, Li Y, Cao R, Zheng G, Huang N*, Zhou Y*. Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. J Chem Inf Model. 2020 Jun 22;60(6):3287-3294.

16. Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, Shimazaki M, Minami A, Oikawa H, Huang N, Houk KN, Huang L, Dai J, Lei X. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nat Chem. 2020 Jul;12(7):620-628.

17. Ju D, Zhang W, Yan J, Zhao H, Li W, Wang J, Liao M, Xu Z, Wang Z, Zhou G, Mei L, Hou N, Ying S, Cai T, Chen S, Xie X, Lai L, Tang C, Park N, Takahashi JS, Huang N, Qi X, Zhang EE. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci Transl Med. 2020 May 6;12(542):eaba0769.

18. Yang J, Shen C, Huang N. Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets. Front Pharmacol. 2020 Feb 25;11:69.

19. Lin H, Zhang X, Liu L, Fu Q, Zang C, Ding Y, Su Y, Xu Z, He S, Yang X, Wei X, Mao H, Cui Y, Wei Y, Zhou C, Du L, Huang N, Zheng N, Wang T, Rao F. Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome. Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4117-4124.

20. Peng S, Li W, Hou N, Huang N. A Review of FoxO1-Regulated Metabolic Diseases and Related Drug Discoveries. Cells. 2020 Jan 10;9(1). pii: E184.

21. Li G, Li W, Xie Y, Wan X, Zheng G, Huang N*, Zhou Y*. Discovery of Novel Pim-1 Kinase Inhibitors with a Flexible-Receptor Docking Protocol. J Chem Inf Model. 2019 Oct 28;59(10):4116-4119.

22. Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun. 2019 Sep 2;10(1):3911.

23. Wang Y, Fu Q, Zhou Y, Du Y, Huang N. Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions. J Chem Inf Model. 2019 Jul 22;59(7):3136-3143

24. Peng S, Xiao W, Ju D, Sun B, Hou N, Liu Q, Wang Y, Zhao H, Gao C, Zhang S, Cao R, Li P, Huang H, Ma Y, Wang Y, Lai W, Ma Z, Zhang W, Huang S, Wang H, Zhang Z, Zhao L, Cai T, Zhao Y, Wang F, Nie Y, Zhi G, Yang YG*, Zhang EE*, Huang N*. Identification of Entacapone as a Chemical Inhibitor of FTO Mediating Metabolic Regulation through FOXO1. Sci. Transl. Med., 2019, 11(488) :eaau7116.

25. Zhang C, Qin S, Hu B, Lv J, Yang Z, Yan W, Wang J, Huang N, Huang Z. Disruption of nucleobase stacking to restore reactivity. Nucleosides Nucleotides Nucleic Acids. 2019 Mar 28:1-11.

26. Sun L, Ma L, Zhang H, Cao Y, Wang C, Hou N, Huang N, von Deneen KM, Zhao C, Shi Y, Pan Y, Wang M, Ji G, Nie Y. Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota. Theranostics. 2019 Jan 24;9(3):721-733.

27. Wang Y, Du Y, Huang N. A survey of the role of nitrile groups in protein-ligand interactions. Future Med Chem. 2018 Dec;10(23):2713-2728.

28. Zhou Y, Wang Y, Li P, Huang XP, Qi X, Du Y*, Huang N*. Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor-Ligand Interactions. ACS Med Chem Lett. 2018 Oct 1;9(10):1019-1024.

29. Lei Z, Chai N, Tian M, Zhang Y, Wang G, Liu J, Tian Z, Yi X, Chen D, Li X, Yu P, Hu H, Xu B, Jian C, Bian Z, Guo H, Wang J, Peng S, Nie Y, Huang N, Hu S, Wu K. Novel peptide GX1 inhibits angiogenesis by specifically binding to transglutaminase-2 in the tumorous endothelial cells of gastric cancer. Cell Death Dis. 2018 May 21;9(6):579.

30. Ren S, Caforio A, Yang Q, Sun B, Yu F, Zhu X, Wang J, Dou C, Fu Q, Huang N, Sun Q, Nie C, Qi S, Gong X, He J, Wei Y, Driessen AJ, Cheng W. Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Res. 2017 Nov;27(11):1378-1391.

31. Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X*, Huang N*. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. J Med Chem. 2017 Oct 26;60(20):8552-8564.

32. Zhang L, Sun H, Chen Z, Liu Z, Huang N*, Qian F*. Intermolecular Interactions between Coencapsulated Drugs Inhibit Drug Crystallization and Enhance Colloidal Stability of Polymeric Micelles. Mol Pharm. 2017 Oct 2;14(10):3568-3576.

33. Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 2017, 27(5):606-625.

34. Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. Structure of protein O-mannose kinase reveals a unique active site architecture. Elife. 2016, 5. pii: e22238.

35. Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angew Chem Int Ed Engl. 2016, 55(46):14330-14334.

36. Liu JJ, Niu CY, Wu Y, Tan D, Wang Y, Ye MD, Liu Y, Zhao W, Zhou K, Liu QS, Dai J, Yang X, Dong MQ, Huang N, Wang HW. CryoEM structure of yeast cytoplasmic exosome complex. Cell Res. 2016, 26(7):822-37.

37. Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. Mol Cell. 2016, 61(4):507-19.

38. Yu Zhou, Jing Ma, Xinyu Lin, Xiping Huang, Kaichun Wu* and Niu Huang*. Structure-Based Discovery of Novel and Selective 5-Hydroxytryptamine 2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome. J. Med. Chem. 2016, 59(2):707-20.

39. Ran Cao, Yanli Wang and Niu Huang. Discovery of 2-Acylaminothiophene-3- Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules. J Chem Inf Model. 2015, 55(11):2435-42.

40. Hu Z, Wan X, Hao R, Zhang H, Li L, Li L, Xie Q, Wang P, Gao Y, Chen S, Wei M, Luan Z, Zhang A, Huang N, Chen L. Phosphorylation of mutationally introduced tyrosine in the activation loop of HER2 confers gain-of-function activity. PLoS One. 2015,10(4):e0123623.

41. Dong T, Li C, Wang X, Dian L, Zhang X, Li L, Chen S, Cao R, Li L, Huang N, He S, Lei X. Ainsliadimer A selectively inhibits IKKα/β by covalently binding a conserved cysteine. Nat Commun. 2015, 6:6522.

42. Yu Zhou and Niu Huang. Binding site druggability assessment in fragment-based drug design. Methods Mol. Biol. 2015, 1289:13-21.

43. Yao Q, Zhang L, Wan X, Chen J, Hu L, Ding X, Li L, Karar J, Peng H, Chen S, Huang N, Rauscher FJ, Shao F. (2014) Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway. PLoS Pathog. 2014, 10(11): e1004522.

44. Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, Shao F. A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Elife 2014, 3: 03714.

45. Ran Cao, Niu Huang and Yanli Wang. Evaluation and application of MD-PB/SA in structure-based hierarchical virtual screening. J Chem Inf Model. 2014, 54:1987-96.

46. Deng M, Lu Z, Zheng J, Wan X, Chen X, Hirayasu K, Sun H, Lam Y, Chen L, Wang Q, Song C, Huang N, Gao GF, Jiang Y, Arase H, Zhang CC. A motif in LILRB2 critical for Angptl2 binding and activation. Blood. 2014, 124:924-35.

47. Yu Zhou, Chao Wu, Lifeng Zhao and Niu Huang. Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin. Proteins. 2014, 82:2412-28.

48. Hanzi Sun, Lifeng Zhao, Shiming Peng and Niu Huang. Incorporating Replacement Free Energy of Binding-site Waters in Molecular Docking. Proteins. 2014, 82:1765-76.

49. Wei Li, Xiaobo Wan, Wei Zhang, Fanqi Zeng, Yanli Wang, Yuting Xie, Li Li and Niu Huang. More than just GPCR Ligand: Structure-based Discovery of Thioridazine Derivatives as Pim-1 Kinase Inhibitors. Med. Chem.Commun. 2014, 5:507-511.

50. Ran Cao, Wei Li, Hanzi Sun, Yu Zhou and Niu Huang. Computational chemistry in structure-based drug design. Acta Pharmaceutica Sinica. 2013, 48:1041-1052.

51. Shiming Peng, Yu Zhou and Niu Huang. Improving the accuracy of pose prediction in molecular docking via structural filtering and conformational clustering. Chinese Chem. Lett. 2013, 24:1001-1004.

52. Fanqi Zeng, Shiming Peng, Li Li, Libing Mu, Zhenghua Zhang, Zhiyuan Zhang and Niu Huang. HAT off: structure-based identification of drug-like inhibitors of p300 histone acetyltransferase. Acta Pharmaceutica Sinica. 2013, 48:700-708.

53. Xiaobo Wan, Yue Ma, Christopher L. McClendon, Lily Jun-shen Huang* and Niu Huang*. Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure. PLoS Comp. Biol. 2013, 9: e1003022.

54. Xiaobo Wan, Wei Zhang, Li Li, Yuting Xie, Wei Li and Niu Huang. A New Target for An Old Drug: Identifying Mitoxantrone as a Nanomolar Inhibitor of PIM1 Kinase via Kinome-wide Selectivity Modeling. J. Med. Chem. 2013, 56:2619-29.

55. Yao Wu, Xiaodong Dai, Niu Huang* and Lifeng Zhao*. A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space. J. Comp. Chem. 2013, 34:1271-82.

56. Yanli Wang, Minyu Liu, Ran Cao, Ming Yin, Riuhua Xiao, Quanhai Liu* and Niu Huang*. A Soluble Bis-chelated Gold(I) Diphosphine Compound with Strong Anticancer Activity and Low Toxicity. J. Med. Chem. 2013, 56: 1455-66.

57. Qing Yao, Jixin Cui, Jiayi Wang, Ting Li, Xiaobo Wan, Tianming Luo, Yi-Nan Gong, Ying Xu, Niu Huang and Feng Shao. Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Proc. Natl. Acad. Sci. U S A. 2012, 109:20395-400.

58. Ran Cao, Minyu Liu, Min Yin, Quanhai Liu, Yanli Wang and Niu Huang. Discovery of Novel Tubulin Inhibitors via Structure-Based Hierarchical Virtual Screening. J. Chem. Inf. Model. 2012, 52:2730-40.

59. Shiming Peng, Xingyu Lin, Zongru Guo and Niu Huang. Identifying Multiple-Target Ligands via Computational Chemogenomics Approaches. Curr. Top. Med. Chem. 2012, 12:1363-1375.

60. Xingyu Lin, Xiping Huang, Gang Chen, Ryan Whaley, Shiming Peng, Yanli Wang, Guoliang Zhang, Shaohui Wang, Xiang Wang, Brian Roth and Niu Huang. Life Beyond Kinases: Structure-Based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors. J. Med. Chem. 2012, 55:5749-59. (Selected by F1000 Pharmacology & Drug Discovery, Congreve M: 2012. http://f1000.com/717951322)

61. Chen P, Song Z, Qi Y, Feng X, Xu N, Sun Y, Wu X, Yao X, Mao Q, Li X, Dong W, Wan X, Huang N, Shen X, Liang Z, Li W. Molecular determinants of enterovirus 71 viral entry: cleft around GLN-172 on VP1 protein interacts with variable region on scavenge receptor B 2. J. Biol. Chem. 2012, 287:6406-20.

62. Andrew Christofferson and Niu Huang. How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries. Methods in Molecular Biology. 2012. 819:187-95.

63. Lifeng Zhao, Chuanjie Wu and Niu Huang. Mutual Solubilities Study for Binary Mixtures of Dipropylene Glycol Dimethyl Ether and Water via Molecular Dynamics Simulation and AMOEBA Polarizable Force Field. Fluid. Phase. Equilib. 2011, 310: 32-8.

64. Andrew Christofferson, Lifeng Zhao, Hanzi Sun, Zhen Huang and Niu Huang. Theoretical Studies of the Base Pair Fidelity of Selenium-modified DNA. J. Phys. Chem B. 2011, 115:10041-8.

65. Qiang Pei, Andrew Christofferson, Hui Zhang, Jijie Chai and Niu Huang. Computational Investigation of the Enzymatic Mechanisms of Phosphothreonine Lyase. Biophys. Chem. 2011, 157:16-23.

66. Niu Huang* and Matthew P. Jacobson. Binding-Site Assessment by Virtual Fragment Screening. PLoS ONE. 2010, 5: e10109

67. John Irwin, Brian Shoichet, Michael Mysinger, Niu Huang, Francesco Colizzi, Pascal Wassam and Yiqun Cao. Automated docking screens: a feasibility study. J. Med. Chem. 2009, 52:5712-20

68. Chaya S. Rapp, Cheryl Schonbrun, Matthew P. Jacobson, Chakrapani Kalyanaraman and Niu Huang. Automated Site Preparation in Rescoring of Receptor Ligand Complexes. Proteins. 2009, 77:52-61

69. Qing Yao, Jixin Cui, Yongqun Zhu, Guolun Wang, Liyan Hu, Chengzu Long, Ran Cao, Xinqi Liu, Niu Huang, She Chen, Liping Liu and Feng Shao. A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle. Proc. Natl. Acad. Sci. U S A. 2009, 106:3716-3721

70. Zhiwei Huang, Yingcai Feng, Xiaojing Wu, Xiaojun Wang, Xingguo Xiao, Wenhui Li, Niu Huang, Lichuan Gu, Guangming Zhong and Jijie Chai. Structural and biochemical mechanisms of the catalysis, activation and inhibition of CPAF (Chlamydial Protease/Proteasome-like Activity Factor). Cell Host & Microbe. 2008, 4: 529-542

71. Niu Huang and Brian Shoichet. Exploring Ordered Waters in Molecular Docking. J. Med. Chem. 2008, 51:4862-4865

72. Linjie Chen, Huayi Wang, Jie Zhang, Lichuan Gu, Niu Huang, Jian-Min Zhou and Jijie Chai. Structural basis for the catalytic mechanism of phosphothreonine lyase. Nat. Struct. Mol. Biol. 2008, 15:101-102

73. Niu Huang and Matthew P. Jacobson. Physics-based Methods for Studying Protein-Ligand Interactions. Curr. Opin. Drug Discov. Devel. 2007, 10:325-331.

74. Niu Huang, John Irwin and Brian Shoichet. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49:6789-6801.

75. Niu Huang, Chakrapani Kalyanaraman, Katarzyna Bernacki and Matthew P. Jacobson. Ligand Binding Free-energy Calculations via Physics-based Scoring Methods. Phys. Chem. Chem. Phys. 2006, 8:5166-5177.

76. Nilesh K. Banavali, Niu Huang and Alexander D. MacKerell, Jr. Conserved Patterns in Backbone Torsion Changes Allow For Single Base Flipping from Duplex DNA with Minimal Distortion of the Double Helix. J. Phys. Chem. B. 2006, 110:10997-11004.

77. Niu Huang, Chakrapani Kalyanaraman, John Irwin, Matthew P. Jacobson. Physics-based Scoring of Protein-ligand Complexes: Enrichment of known inhibitors in Large-Scale Virtual Screening. J. Chem. Inf. Model. 2006, 46:243-253.

78. Victor M. Anisimov, Guillaume Lamoureux, Igor V. Vorobyov, Niu Huang, Benoit Roux, Alexander D. MacKerell, Jr. Determination of Electrostatic Parameters for a polarizable Force Field Based on the Classical Drude Oscillator. J. Chem. Theory. Comp. 2005, 1: 153-168.

79. Niu Huang and Alexander D. MacKerell, Jr. Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J. Mol. Biol. 2005, 345:265-274.

80. John R. Horton, Gary Ratner, Nilesh K. Banavali, Niu Huang, Yongseok Choi, Martin A. Maier, Victor E. Marquez, Alexander D. MacKerell, Jr., Xiaodong Cheng. Caught in the Middle of the Act: Visualization of a Putative Transition State During DNA Base Flipping. Nucl. Acids. Res. 2004, 32: 3877-3886.

81. Niu Huang, Ashish Nagarsekar, Guanjun Xia, Jun Hayashi and Alexander D. MacKerell, Jr. Identification of Non-Phosphate-Containing Small Molecular Weight Inhibitors of the Tyrosine Kinase p56 Lck SH2 Domain via in Silico Screening against the pY+3 Binding Site. J. Med. Chem. 2004, 47 (14):3502-3511.

82. Niu Huang and Alexander D. MacKerell, Jr. Atomistic view of Base flipping in DNA. Phil. Trans. Roy. Soc. Lond. Series A. 2004, 362: 1-22.

83. Hui Peng#, Niu Huang#, Jing Qi, Ping Xie, Chen Xu, Jianxiang Wang and Chunzheng Yang. Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening. Bioorg. Med. Chem. Lett. 2003, 13(21):3693-3699.

84. Niu Huang, Nilesh K. Banavali and Alexander D. MacKerell, Jr. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. U S A, 2003, 100: 68-73.

85. Yongping Pan, Niu Huang, Sam Cho and Alexander D. MacKerell, Jr. Consideration of Molecular Weight During Compound Selection in Virtual Target-Based Database Screening. J. Chem. Inf. Comput. Sci. 2003;43(1); 267-272

86. Niu Huang and Alexander D. MacKerell, Jr. An Ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest. J. Phys. Chem A, 2002, 106: 7820-7827.

87. Niu Huang, Linbo Qu, Qiqing Zhu, Fengming Chu, Guangzhong Yang and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: Molecular Modeling of Interaction between Selective Retinoids Nuclear Receptors. Acta Pharmaceutica Sinica.1999, 34: 358-362

88. Niu Huang, Fengmin Chu and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: Hansch Analysis and 3D-QSAR Studies on Specific Ligands of Retinoid X Receptor. Acta Pharmaceutica Sinica. 1998, 33: 442-448

89. Qiqin Zhu, Zongru Guo, Niu Huang, Minmin Wang, and Fengming Chu. Comparative Molecular Field Analysis of a Series of Taxol Analogues. J. Med. Chem, 1997, 40: 4319-4328

90. Minmin Wang, Niu Huang, Guangzhong Yang and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: II. 3D-QSAR of Retinoids and Receptor Interaction. Acta Pharmaceutical Sinica. 1997, 32(1): 43-48

91. Niu Huang, Minmin Wang, Fengmin Chu and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: I. 3D-QSAR of Retinoidal Anti-Carcinogenic Activities. Acta Pharmaceutica Sinica. 1996, 31(12): 932-939

1994	南開大學物理系生物物理學學士學位
	Bachelor of Biophysics，Department of Physics University of Nankai,?Tianjin,
2003	馬里蘭大學巴爾的摩分校藥學博士學位
	Ph.D.，Department of Pharmaceutical Sciences，University ofMaryland at Baltimore

2013年	北京生命科學研究所高級研究員
	Associate Investigator, National Institute of Biological Sciences, Beijing, China
2007-2012年	北京生命科學研究所研究員
	Assistant Investigator, National Institute of Biological Sciences, Beijing, China
2003-2007年	加利福尼亞大學舊金山分校藥物化學系和生物醫藥學系博士后
	Postdoctoral associate, Depts. of Pharmaceutical Chemistry and Biopharmaceutical Sciences, University of California at San Francisco
1994-1998年	中國醫學科學院&中國協和醫科大學藥物研究所研究助理
	Research assistant, Institute of Materia Medica, Peking Union of Medical College & Chinese Academy of Medical Sciences