1. 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, In press.
2. 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, In press.
3. 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, Feb 26. [Epub ahead of print]
4. 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, Feb 19. [Epub ahead of print]
5. 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, Jan 30. [Epub ahead of print]
6. Yao Q, Cui J, Wang J, Li T, Wan X, Luo T, Gong YN, Xu Y, Huang N, Shao F. Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Proc Natl Acad Sci U S A. 2012 Nov 21. [Epub ahead of print]
7. Ran Cao, Minyu Liu, Min Yin, Quanhai Liu, Yanli Wang, Niu Huang. Discovery of Novel Tubulin Inhibitors via Structure-Based Hierarchical Virtual Screening.J. Chem. Inf. Model. 2012.
8. Shiming Peng, Xingyu Lin, Zongru Guo, Niu Huang. Identifying Multiple-Target Ligands via Computational Chemogenomics Approaches. Curr. Top. Med. Chem. 2012, 12:1363-1375.
9. Xingyu Lin, Xiping Huang, Gang Chen, Ryan Whaley, Shiming Peng, Yanli Wang, Guoliang Zhang, Shaohui Wang, Xiang Wang, Brian Roth, 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 ).
10. 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. Book
11. 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.
12. 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.
13. Qiang Pei, Andrew Christofferson, Hui Zhang, Jijie Chai, Niu Huang, Computational Investigation of the Enzymatic Mechanisms of Phosphothreonine Lyase, Biophysical Chemistry. 2011;157(1-3):16-23.
14. Niu Huang and Matthew P. Jacobson. Binding-Site Assessment by Virtual Fragment Screening. PLoS ONE. 2010, 5: e10109
15. 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
16. 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
17. 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
18. 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
19. Niu Huang and Brian Shoichet. Exploring Ordered Waters in Molecular Docking. J. Med. Chem. 2008, 51:4862-4865.
20. 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
21. Niu Huang and Matthew P. Jacobson. Physics-based Methods for Studying Protein-Ligand Interactions. Curr. Opin. Drug Discov. Devel. 2007, 10:325-331.
22. Niu Huang, John Irwin and Brian Shoichet. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49: 6789-6801.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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: 3502-3511.
30. 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.
31. 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: 3693-3699. * equal contribution
32. Niu Huang, Nilesh K. Banavali and Alexander D. MacKerell, Jr. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. PNAS, 2003, 100: 68-73.
33. 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: 267-272
34. 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.
35. 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
36. 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
37. 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
38. 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: 43-48
39. 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: 932-939