Shijun Zhong, Ph.D. Professor of computational chemistry sjzhong at dlut.edu.cn http://faculty.dlut.edu.cn/2011011110 Research Field: Computational Chemistry and Computational Biology Enrollment Information: Master Degree Candidates in physical chemistry (School of Chemistry), biochemistry, biochemical engineering, bioengineering and biotechnology. Doctoral Candidates in physical chemistry (School of Chemistry), biochemical engineering, bioengineering and biotechnology. Selected Publication: 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: 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. 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. 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. 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. 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. 33. Zhong, S.; Zhang, Y.; Xiu, Z., Rescoring ligand docking poses, Curr. Opin. Drug Discov. Devel., 2010, 13 (3), 326-334. 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. 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. 构建了一些药物小分子的CHARMM力场 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. 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. 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. 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. 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. (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. 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 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. 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. 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