研究领域:
计算化学与计算生物学，含量子化学、分子动力学模拟、计算机辅助药物设计。我们发展和使用这些领域的方法，研究化学和生物大分子之间以及与小分子的相互作用。探索功能分子设计，如催化剂的理性设计。研究调控生物体系过程的途径，包含机理研究、新药设计等。

研究方向:
1、生物大分子之间以及与小分子的相互作用
2、量子化学精确计算与分块化计算
3、计算机辅助药物设计
4、环境治理催化材料的理性设计和数据库建设

招生专业:
1、物理化学 (专业代码: 070304 , 在化学学院招生)
2、生物化工 (专业代码: 081703 , 在生命科学与技术学院招生)
3、生物工程与技术 (专业代码: 0831Z2 , 在生命科学与技术学院招生)
4、生物学

课题组情况：
1，在读：4名博士生，5名硕士生。
2，毕业：1名访问学者，1名博士后，6名硕士。
3，经费：1项国家自然科学基金重点项目（2016-2020）。

论文选列：
Book Chapter:
34. Zhong,S,; Oashi, T.; Yu, W.; Shapiro, P.; and MacKerell, A.D., Jr., (2012) Prospects of Modulating Protein-Protein Interactions, in Protein-Ligand Interactions, First Edition (ed Holger Gohlke), (the 53th book in the series: Methods and Principles in Medicinal Chemistry), Wiley-VCH, Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527645947.ch15, p295-329.

Patent:
35. Tomkinson, A.; Chen, X.; Dziegielewska, B.; MacKerell, A. D.; Zhong, S.; Wilson, G., Compounds that Inhibit Human DNA Ligases and Methods of Treating Cancer. The World Intellectual Property Organization, Patent No.: US 8,445,537 B2, Date of Patent: May 21, 2013.

Articles:

52. Sun L, Zhang CH, Chen JM, Zhao XQ, Bai FW, Zhong SJ, Combining oligomer build-up with alanine scanning to determine the flocculation protein mutants for enhancing oligosaccharide binding. Mol Simulat 2022, 48 (4):330-341. https://doi.org/10.1080/08927022.2021.2015068

51. Chu H, Zhao Q, Shan Y, Zhang S, Sui Z, Li X, Fang F, Zhao B, Zhong S, Liang Z, Zhang L, Zhang Y, All-Ion Monitoring-Directed Low-Abundance Protein Quantification Reveals CALB2 as a Key Promoter in Hepatocellular Carcinoma Metastasis. Anal Chem 2022, 94 (16):6102-6111. https://doi.org/10.1021/acs.analchem.1c03562 

50. Chu H, Zhao Q, Liu J, Yang K, Wang Y, Liu J, Zhang K, Zhao B, He H, Zheng Y, Zhong S, Liang Z, Zhang L, Zhang Y, Ionic Liquid-Based Extraction System for In-Depth Analysis of Membrane Protein Complexes. Anal Chem 2022, 94 (2):758-767. https://doi.org/10.1021/acs.analchem.1c03195 

49. Zhao D, Zhong SJ, Binding mechanisms of varic acid inhibitors on protein tyrosine phosphatase 1B and in silico design of the novel derivatives. Mol Simulat 2021, 47 (9):771-784. https://doi.org/10.1080/08927022.2021.1929970 

48. Zhao D, Sun L, Zhong SJ, Discovery of inhibitors targeting protein tyrosine phosphatase 1B using a combined virtual screening approach. Mol Divers 2021, 26 (4):2159-2174. https://doi.org/10.1007/s11030-021-10323-2 

47. Sun L, Fu TT, Zhao D, Fan HJ, Zhong SJ, Divide-and-link peptide docking: a fragment-based peptide docking protocol. Phys Chem Chem Phys 2021, 23 (39):22647-22660. https://doi.org/10.1039/d1cp02098f 

46. Sun L, Fan H, Zhong S, Evaluating the covalent binding of carbapenems on BlaC using noncovalent interactions. Journal of molecular modeling 2021, 27 (6):161. https://doi.org/10.1007/s00894-021-04760-x 

45. Jiang JP, Yang M, Cao XP, Wan HH, Liu SQ, Zhong SJ, Yan JY, Xue S, A Novel Material for Selective Separation of Monogalactosyldiacylglycerols from Microalgae. J Ocean U China 2021, 20 (1):221-227. https://doi.org/10.1007/s11802-021-4504-y 

44. Chu H, Wu C, Zhao Q, Sun R, Yang K, Zhao B, Liu Y, Liang Z, Zhong S, Zhang L, Zhang Y, Quantitative proteomics identifies FOLR1 to drive sorafenib resistance via activating autophagy in hepatocellular carcinoma cells. Carcinogenesis 2021, 42 (5):753-761. https://doi.org/10.1093/carcin/bgab019 

43. Gao JQ, Feng HL, Yuan WJ, Li YM, Hou SB, Zhong SJ, Bai FW, Enhanced fermentative performance under stresses of multiple lignocellulose-derived inhibitors by overexpression of a typical 2-Cys peroxiredoxin from Kluyveromyces marxianus. Biotechnol Biofuels 2017, 10. https://doi.org/10.1186/s13068-017-0766-4   

42. Gao JQ, Yuan WJ, Li YM, Bai FW, Zhong SJ, Jiang Y, Application of redox potential control to improve ethanol productivity from inulin by consolidated bioprocessing. Process Biochem 2016, 51 (10):1544-1551. https://doi.org/10.1016/j.procbio.2016.07.011 

41. Gao J, Yuan W, Li Y, Xiang R, Hou S, Zhong S, Bai F, Transcriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology. Biotechnol Biofuels 2015, 8:115. https://doi.org/10.1186/s13068-015-0295-y 

40. Yu, H.; Lu, Y.; Qiao, X.; Wei, L.; Fu, T.; Cai, S.; Wang, C.; Liu, X.; Zhong, S.; Wang, Y., Novel Cathelicidins from Pigeon Highlights Evolutionary Convergence in Avain Cathelicidins and Functions in Modulation of Innate Immunity. Sci Rep 2015, 5, 11082. https://doi.org/10.1038/srep11082 

39. Li, T.; He, X.; Thomas, J. M.; Yang, D.; Zhong, S.; Xue, F.; Smith, W. W., A novel GTP-binding inhibitor, FX2149, attenuates LRRK2 toxicity in Parkinson's disease models. PLoS One 2015, 10, (3), e0122461. https://doi.org/10.1371/journal.pone.0122461

38. Gao, J.; Yuan, W.; Kong, L.; Xiang, R.; Zhong, S., Efficient ethanol production from inulin by two-stage aerate strategy. biom. bioe. 2015, 80, 10-16. 

https://doi.org/10.1016/j.biombioe.2015.04.013

37. Chu, Y.; Sun, L.; Zhong, S., How Y357F, Y276F mutants affect the methylation activity of PRDM9: QM/MM MD and free energy simulations. J Mol Model 2015, 21, (5), 125. https://doi.org/10.1007/s00894-015-2673-6  酶催化下的甲基化机理计算
36. Li, T.; Yang, D.; Zhong, S.; Thomas, J. M.; Xue, F.; Liu, J.; Kong, L.; Voulalas, P.; Hassan, H. E.; Park, J. S.; MacKerell, A. D., Jr.; Smith, W. W., Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models. Hum Mol Genet 2014, 23 (23), 6212-22. https://doi.org/10.1093/hmg/ddu341 

33. Zhong, S.; Zhang, Y.; Xiu, Z., Rescoring ligand docking poses, Curr. Opin. Drug Discov. Devel., 2010, 13 (3), 326-334. https://pubmed.ncbi.nlm.nih.gov/20443166/  分析如何优化蛋白质与小分子结合的打分函数
32. Cerchietti, L. C.; Ghetu, A. F.; Zhu, X.; Da Silva, G. F.; Zhong, S.; Matthews, M.; Bunting, K. L.; Polo, J. M.; Fares, C.; Arrowsmith, C. H.; Yang, S. N.; Garcia, M.; Coop, A.; Mackerell, A. D., Jr.; Prive, G. G.; Melnick, A., A Small-Molecule Inhibitor of BCL6 Kills DLBCL Cells In Vitro and In Vivo. Cancer Cell, 2010, 17(4), 400-411. https://doi.org/10.1016/j.ccr.2009.12.050 从计算到获得蛋白质-小分子复合物晶体
31. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; Mackerell, A. D., Jr., CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields. J. Comput. Chem. 2010, 31 (4), 671-690. 

https://doi.org/10.1002/jcc.21367   构建了一些药物小分子的CHARMM力场

30. Sorci L, Pan Y, Eyobo Y, Rodionova I, Huang N, Kurnasov O, Zhong S, MacKerell AD, Jr., Zhang H, Osterman AL, Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol 2009, 16 (8):849-861. https://doi.org/10.1016/j.chembiol.2009.07.006 

28. Zhong, S.; Barnes, E.C. and Petersson, G.A., Uniformly Convergent n-tuple-Zeta Augmented Polarized (nZaP) Basis Sets for CBS Extrapolations. I. Atomic SCF Energies. J. Chem. Phys. 2008, 129, 184116. https://doi.org/10.1063/1.3009651  构建了最精确而不多耗时的量子化学基组，与Gaussian软件合作

27. Zhong, S.; Chen, X.; Zhu, X.; Dziegielewska, B.; Ellenberger, T.; Wilson, G.M.; Tomkinson, A.E.; MacKerell, Jr., A.D., Identification and validation of human DNA ligase inhibitors using computer-aided drug design, J. Med. Chem. 2008, 51(15), 4553-4562. https://doi.org/10.1021/jm8001668  计算与实验配合，设计并确定了DNA链接酶的抑制剂
26. Zhong, S.; MacKerell, Jr., A.D., Pose scaling: Geometrical assessment of ligand binding poses. J. Theor. Comput. Chem. 2008, 7(4), 833-852. https://doi.org/10.1142/S0219633608004155  一种标度方法，结合能量与几何选位 来改进小分子在蛋白质表面结合的打分函数
25. Chen, X.; Zhong, S.; Zhu, X.; Dziegielewska, B.; Ellenberger, T.; Wilson, G. M.; MacKerell, A. D., Jr.; Tomkinson, A. E., Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res. 2008, 68, (9), 3169-3177. https://doi.org/10.1158/0008-5472.CAN-07-6636  计算与实验相结合的药物设计研究
24. Zhong, S.; MacKerell, Jr., A. D. Binding response: A descriptor for selecting ligand binding site on protein surfaces. J. Chem. Inf. Model. 2007, 47 (6), 2303-2315.
https://doi.org/10.1021/ci700149k  (Journal Cover Figure) 一种确定蛋白质表面活性位的方法，可直接与分子对接软件配合
22. Zhong, S.; Macias, A. T.; MacKerell, A. D., Computational identification of inhibitors of protein-protein interactions. Curr. Top. Med. Chem. 2007, 7, (1), 63-82. https://doi.org/10.2174/156802607779318334  分析计算机辅助药物设计的各个环节，并给出了一套成熟的方案

21. Chen F, Hancock CN, Macias AT, Joh J, Still K, Zhong S, MacKerell AD, Jr., Shapiro P (2006) Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure. Bioorg Med Chem Lett 16 (24):6281-6287. https://doi.org/10.1016/j.bmcl.2006.09.038

20. Shiozuka M, Shimada K, Zhong SJ, MacKerell A, Matsuda R, The chemotherapeutic agents for readthrough of nonsense mutations. Zoological Science 2006, 23 (12):1165-1165.

19. Petersson, G. A.; Zhong, S. ; Montgomery, J. A.; Frisch, M. J., On the Optimization of Gaussian Basis Sets. J. Chem. Phys. 2003, 118 (3), 1101-1109. https://doi.org/10.1063/1.1516801  使用多项式来优化量子化学高斯基组
18. Zhong, S.; Dadarlat, V. M.; Glaeser, R. M.; Head-Gordon, T.; Downing, K. H, Modeling chemical bonding effects for protein electron crystallography: the Transferable Fragmental Electrostatic Potential (TFESP) Method. Acta Crystallogr. A 2002, 58, 162-170. https://doi.org/10.1107/s0108767301020256  发展了分块化方案来计算蛋白质的分子静电势，以改进电子衍射构建的蛋白质结构模型
17. Wu, W.; Zhong, S.; Shaik, S., VBDFT(s): a Huckel-type semi-empirical valence bond method scaled to density functional energies. Application to linear polyenes. Chem. Phys. Lett. 1998, 292, (1-2), 7-14. 用密度泛函理论的能量来标度的一种价键理论方法
15. Zhong, S.; Wang, Y.; Zhang, Q., Analogy between real irreducible tensor operator and molecular two-particle operator. Theor. Chem. Acc. 1997, 96, (2), 135-139. 把不可约张量算子技巧用于量子化学双电子分子积分
14. Zhong, S.; Liu, C., Possible binding modes for dinitrogen activation by the FeMo-cofactor in nitrogenase. Polyhedron 1997, 16, (4), 653-661. 探索固氮酶辅基固氮活化的模式
13. Zhong, S. ; Liu, C., Stability of X4Y24q (X=C, Si; Y=B, Al, C, Si, N, P; q=-4 to 4) and C28X4 (X=H, F, Cl, Br, I). J. Mol. Struc-Theochem. 1997, 392, 125-136. 混杂团簇小分子的稳定性
12. Shi, J.; Wen, T.; Zheng, Y.; Zhong, S. ; Wu, D.; Liu, Q.; Kang, B.; Wu, B.; Mak, T. C. W., Palladium complexes with simultaneous O:S coordination, syntheses, structures and characterization of complexes with 2-mercaptophenol or 2-mercaptopyridine N-oxide. Polyhedron 1997, 16, (3), 369-375. 计算与实验相结合研究过渡金属原子配合物
11. Zhong, S. ; Wang, Y.; Zhang, Q., Symmetry reduction of the matrix elements of a two-particle operator. Int. J. Quantum Chem. 1996, 60, (4), 833-841. 利用分子对称性简化量子化学双电子分子积分的计算
10. Zhong, S. ; Wang, Y.; Zhang, Q., Real irreducible tensorial sets. Int. J. Quantum Chem. 1996, 59, (3), 173-182 建立了不可约张量集的实基体系，用于构造量子化学中的轨道