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梅晔

职称:

直属机构: 精密光谱科学与技术国家重点实验室

学科:

10 访问

相关教师

个人资料

  • 部门: 精密光谱科学与技术国家重点实验室
  • 性别:
  • 专业技术职务: 教授
  • 毕业院校: 南京大学
  • 学位: 理学博士
  • 学历: 研究生
  • 联系电话:
  • 电子邮箱: samuel.y.mei@gmail.com
  • 办公地址: 中山北路校区理科大楼A1012
  • 通讯地址: 上海市中山北路3663号华东师范大学精密光谱科学与技术国家重点实验室
  • 邮编: 200062
  • 传真:

教育经历

理学学士,南京大学基础学科教学强化部,1998年9月--2002年6月

理学博士,南京大学化学化工学院,2002年9月--2007年6月

工作经历

研究员 2012年8月至今

华东师范大学精密光谱科学与技术国家重点实验室


兼职教授2017年9月-11月

俄克拉荷马大学化学和生物化学系


副研究员2009年3月至2012年7月

华东师范大学精密光谱科学与技术国家重点实验室


博士后2007年6月至2009年2月

南京大学物理系


研究助理2005年4月–2005年5月

香港科技大学


访问学者2009年8月至11月

新加坡南洋理工大学


访问副教授2010年10月至2011年1月

新加坡南洋理工大学


访问学者2013年8月至2014年7月

美国国立卫生研究院


个人简介

社会兼职

俄克拉荷马大学化学系和生物化学系兼职教授


研究方向

课题组主页


研究方向

1. 用于蛋白质分子计算机模拟的极化和非极化力场

2. 蛋白质大分子体系的多尺度模拟

3. 计算结构生物学


基金

华东师范大学科研创新基金(2017)
上海市拔尖人才计划(2015)
上海市青年科技启明星项目A类 (2011)
国家自然科学基金委面上项目(2012-2015)
国家自然科学基金委青年项目(2009-2011)
华东师范大学青年创新项目(2011-2012)
江苏省博士后基金
中国博士后基金

团队成员

王晓慧 (博士生2015--)

槐喆 (博士生 2017--)

靳淑伟(硕士生 2018--)

王家宁(硕士生 2018--)

薛园菲 (博士生 2019--)

Group in 2014

毕业成员

陆小亮 (硕士 2010--2013)
郭漫 (硕士2010--2013)
高雅 (博士 2009--2014) 华东师范大学优秀毕业生
曾娟 (博士 2009--2014)
黎永秀 (博士 2011--2014)
牟丽蓉 (硕士 2011--2014)
林冰冰 (硕士 2011--2014)
贾相瑜 (博士 2011--2016) 上海市优秀毕业生
刘凤娇 (博士 2013--2018) 上海市优秀毕业生
柳维 (博士 2013--2019)
王美婷 (博士 2014--2019)
李鹏飞 (博士 2014--2019) 华东师范大学优秀毕业生
童正青(博士 2014--2019)

整理资料(仅供内部使用)

增强采样和自由能计算

https://github.com/samuelymei/freeenergy/blob/master/freeenergy.pdf


开授课程

理论分子生物物理


科研项目

学术成果


Journal Articles

ResearcherIDgoogle scholar


    84. Guo, J.; Yang, L.; Gao, Y.; Zhao, C.; Mei, Y.*; Song, Y.-Y.*, Insight of MOF environment-dependent enzyme activity via MOFs-in-nanochannels configuration, ACS Catalysis, 10, 5949-5958 (2020)

    DOI: 10.1021/acscatal.0c00591

    83. Tong, Z.; Huai, Z.; Mei, Y.; Mo, Y.*, Reproducing the low-temperature excitation energy transfer dynamics of Phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian, Journal of Chemical Physics, 152, 135101 (2020)

    DOI: 10.1063/1.5135999

    82. Shao, Y.*; Mei, Y.; Sundholm, D.*; Kaila, Ville R. I.*, Benchmarking the performance of time-dependent density functional theory methods on biochromophores, Journal of Chemical Theory and Computation16, 587-600 (2020)

    DOI: 10.1021/acs.jctc.9b00823

    81. Zhang, Y.; Liu, W.; Li, Z.; Kumar, V.; Alvarez-Cabrera, A. L.; Leibovitch, E. C.; Cui, Y.; Mei, Y.; Bi, G.-Q.; Jacobson, S.; Zhou, Z. H.*, Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes, Nature Communications, 10, 5346 (2019)
    DOI: 
    10.1038/s41467-019-13064-x

    80. Pan, X.; Li, P.; Ho J.; Pu J.*; Mei, Y.*; Shao, Y.*, Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semiempirical parameters with force matching, Physical Chemistry Chemical Physics, 21, 20595-20605 (2019) (selected as the 2019 PCCP Hot Article)
    DOI: 
    10.1039/C9CP02593F

    79. Liu, W; Li, P.; Mei, Y.*, Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1, Journal of Molecular Modeling, 25, 187 (2019)
    DOI: 
    10.1007/s00894-019-4069-5

    78. Li, P.; Liu, F.; Shao, Y.; Mei, Y.*, Computational insights into endo/exo selectivity of the Diels–Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level, Journal of Physical Chemistry B, 123, 5131-5138 (2019)
    DOI: 
    10.1021/acs.jpcb.9b01989

    77. Qian, J.; Xia, M.X.; Liu, W.; Li, L.J.; Yang, J.; Mei, Y.; Meng, Q.C.; Xie, Yan*, Glabridin resensitizes p-glycoprotein-overexpressing multidrug-resistant cancer cells to conventional chemotherapeutic agents, European Journal of Pharmacology, 852, 231-243 (2019)
    DOI: 
    10.1016/j.ejphar.2019.04.002

    76. Wang, M. T.; Mei, Y.*; Ryde, U.*, Host–guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations, Journal of Chemical Theory and Computation, 15, 2659-2671 (2019)
    DOI: 
    10.1021/acs.jctc.8b01280

    75. Tong, Z.; Huai, Z.; Mei, Y.; Mo, Y.*, Influence of the protein environment on the electronic excitation of chromophores in the phycoerythrin 545 light–harvesting complex: a combined MD-QM/MM method with polarized protein–specific charge scheme, Journal of Physical Chemistry B, 123, 2040-2049 (2019)
    DOI: 
    10.1021/acs.jpcb.8b11764

    74. Liu, W.; Dai, X.; Jih, J.; Chan, K.; Trang, P.; Yu, X.; Balogun, R.; Mei, Y.; Liu, F.; Zhou, Z. H.*, Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein PP150 in murine and human cytomegaloviruses with implications for therapeutic development, PLOS Pathogens, 15, 1-26 (2019)
    DOI: 
    10.1371/journal.ppat.1007615

    73. Wang, M. T.; Mei, Y.*; Ryde, U.*, Predicting relative binding affinity using nonequilibrium QM/MM simulations, Journal of Chemical Theory and Computation, 14, 6613–6622 (2018)
    DOI: 
    10.1021/acs.jctc.8b00685

    72. Li, P.; Jia, X.; Pan, X.; Shao, Y.; Mei, Y.*, Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. weighted thermodynamics perturbation, Journal of Chemical Theory and Computation, 14, 5583–5596 (2018)
    DOI: 
    10.1021/acs.jctc.8b00571

    71. Li, P.; Liu, F.; Jia, X.; Shao, Y.; Hu, W.*; Zheng, J.; Mei, Y.*, Efficient computation of free energy surfaces of Diels–Alder reactions in explicit solvent at ab initio QM/MM level, Molecules, 23, 2487 (2018) (Invited contribution to Special Issue “Combined Quantum Mechanical and Molecular Mechanical Methods and Simulations”)
    DOI: 
    10.3390/molecules23102487

    70. Gao, Y.; Zhu, T.*; Zhang, C.M.; Zhang, J.Z.H.; Mei, Y.*, Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations, Chemical Physics Letters, 706, 594–600 (2018)
    DOI: 
    10.1016/j.cplett.2018.07.014

    69. Li, P. F.; Jia, X. Y.; Wang, M. T.; Mei, Y.*, Comparison of accuracy and convergence rate between equilibrium and nonequilibrium alchemical transformations for calculation of relative binding free energy, Chinese Journal of Chemical Physics, 30, 789−799 (2017) (invited article)
    DOI: 
    10.1063/1674-0068/30/cjcp1711204

    68. Liu, F. J.; Yang, Z. Y.; Yu, Y. M.; Mei, Y.*; Houk, K. N.*, Bimodal Evans–Polanyi relationships in dioxirane oxidations of sp3 C–H: Non-perfect synchronization in generation of delocalized radical intermediates, Journal of the American Chemical Society, 139, 16650–16656 (2017)
    DOI: 
    10.1021/jacs.7b07988

    67. Wang, M. T.; Li, P. F. (co-first author); Jia, X. Y.; Liu, W.; Shao, Y.; Hu, W. X.; Zheng, J.; Brooks, B; Mei, Y.*,  Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical level, Journal of Chemical Information and Modeling, 57, 2476−2489 (2017)
    DOI: 
    10.1021/acs.jcim.7b00001

    66. Sun, Z.*; Zhu, T.; Wang, X.; Mei, Y.; Zhang, JZH*, Optimization of convergence criteria for fragmentation methods, Chemical Physics Letters, 687, 163–170 (2017)
    DOI: 
    10.1016/j.cplett.2017.08.059

    65. Liu, W.; Jia, X. Y.; Wang, M. T.; Li, P. F.; Wang, X. H.; Hu, W. X.; Zheng, J.; Mei, Y.*, Calculations of the absolute binding free energy for Ralstonia Solanacearum Lectins bound with methyl-α-L-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels, RSC Advances, 7, 38570−38580 (2017)
    DOI: 
    10.1039/c7ra06215j

    64. Huang, J.; Mei, Y.; Koenig, G.; Simmonett, A.; Pickard, F.; Wu, Q.; Wang, L.-P.; MacKerell, A.; Brooks, B.; Shao, Y.*, An estimation of hybrid quantum mechanical/molecular mechanical (QM/MM) polarization energies for small molecules using polarizable force-field approaches, Journal of Chemical Theory and Computation, 13, 679−695 (2017)
    DOI: 
    10.1021/acs.jctc.6b01125

    63. Gao, Y.*; Zhang, C.; Zhang, J. Z. H.; Mei, Y.*, Evaluation of the coupled two-dimensional main chain torsional potential in modeling intrinsically disordered proteins, Journal of Chemical Information and Modeling, 57, 267–274 (2017)
    DOI: 
    10.1021/acs.jcim.6b00589

    62. Zeng, J.*; Li, Y. X.; Zhang, J. Z. H.; Mei, Y., Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88, Journal of Molecular Modeling, 22, 177 (2016)
    DOI: 
    10.1007/s00894-016-3027-8

    61. Liu, F.J.; Zhang, J. Z. H.; Mei, Y.*, The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations, Scientific Reports, 6, 27190 (2016)
    DOI: 
    10.1038/srep27190

    60. Liu, F. J.; Yang, Z. Y. (co-first author); Mei, Y.; Houk, Kendall N.*, QM/QM’ direct molecular dynamics of water-accelerated Diels-Alder reaction, Journal of Physical Chemistry B, 120, 6250−6254 (2016)
    DOI: 
    10.1021/acs.jpcb.6b02336

    59. Jia, X. Y.; Wang, M. T. (co-first author); Shao, Y.; Koenig, G.; Brooks, B.; Zhang, J. Z. H.; Mei, Y.*, Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics, Journal of Chemical Theory and Computation, 12, 499−511 (2016)
    DOI: 
    10.1021/acs.jctc.5b00920

    58. Koenig, G.; Mei, Y.; Pickard, F.; Simmonett, A.; Miller, B.; Herbert, J.; Woodcock, H. L.; Brooks, B.; Shao, Y.*,  Computation of hydration free energies using the multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) method, Journal of Chemical Theory and Computation, 12, 332−344 (2016)
    DOI: 
    10.1021/acs.jctc.5b00874

    57. Jia, X. Y.; Mei, Y.; Zhang, J. Z. H.; Mo, Y.*, Hybrid QM/MM study of FMO complex with polarized protein-specific charge, Scientific Reports, 5, 17096 (2015)
    DOI: 
    10.1038/srep17096

    56. Mei, Y.*; Simmonett, A. C.; Pickard IV, F. C.; DiStasio Jr., R. A.; Brooks, B. R.; Shao, Y. H.*, Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions, Journal of Physical Chemistry A, 119, 5865-5882 (2015)
    DOI: 
    10.1021/acs.jpca.5b03159 

    55. Gao, Y.; Li, Y. X.; Mou, L. R.; Lin, B. B.; Zhang, J. Z. H.; Mei, Y.*, Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential, Scientific Reports, 5, 10359 (2015)
    DOI: 
    10.1038/srep10359 

    54. Gao, Y.; Li, Y. X.; Mou, L. R.; Hu, W. X.; Zheng, J.; Zhang, J. Z. H.; Mei, Y.*, Coupled two-dimensional main chain torsional potential for protein dynamics II: Performance and validation, Journal of Physical Chemistry B, 119, 4188-4193 (2015)
    DOI: 
    10.1021/jp510215c

    53. Sodt, A.; Mei, Y.; Koenig, G.; Tao, P.; Steele, R.; Brooks, B.; Shao, Y.*, Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. I. Estimation of polarization energies, Journal of Physical Chemistry A, 119, 1511-1523 (2015)
    DOI: 
    10.1021/jp5072296

    52. Duan, L. L.; Gao, Y.; Ji, C. G.; Mei, Y.; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H.*, Energetics of protein backbone hydrogen bonds and their local electrostatic environment, Science China-Chemistry, 57, 1708-1715 (2014)
    DOI: 
    10.1007/s11426-014-5246-0

    51. Li, Y. X.; Zhang, J. Z. H.; Mei, Y.*, Molecular dynamics simulation of protein crystal with polarized protein-specific force field, Journal of Physical Chemistry B, 118, 12326-12335 (2014)
    DOI: 
    10.1021/jp503972j

    50. Ji, C. G.; Mei, Y.*, Some practical approaches to treating electrostatic polarization of proteins, Accounts of Chemical Research, 47, 2795-2803 (2014)
    DOI: 
    10.1021/ar500094n

    49. Duan, L. L.*; Mei, Y.; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H., Protein’s native structure is dynamically stabilized by electronic polarization, Journal of Theoretical and Computational Chemistry, 13, 1440005 (2014)
    DOI: 
    10.1142/S0219633614400057

    48. Mou, L. R.; Jia, X. Y.; Gao, Y.; Li, Y. X.; Zhang, J. Z. H.; Mei, Y.*, Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions, Journal of Theoretical and Computational Chemistry, 13, 1450026 (2014)
    DOI: 
    10.1142/S0219633614500266 

    47. Lin, B. B.; Gao, Y.; Li, Y. X; Zhang, J. Z. H.; Mei, Y.*, Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of Myoglobin, Journal of Molecular Modeling, 20, 2189 (2014)
    DOI: 
    10.1007/s00894-014-2189-5

    46. Koenig, G.*; Pickard IV, F. C.; Mei, Y.; Brooks B. R., Predicting hydration free energies with a hybrid QM/MM approach: An evaluation of implicit and explicit solvation models in SAMPL4, Journal of Computer-Aided Molecular Design, 28, 245-257 (2014)
    DOI: 
    10.1007/s10822-014-9708-4

    45. Jia, X. Y.; Zeng, J.; Zhang, J. Z. H.; Mei, Y.*, Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis, Journal of Computational Chemistry, 35, 737-747 (2014)
    DOI: 
    10.1002/jcc.23547

    44. Jia, X. Y.; Wang, X. W.; Liu, J. F.; Zhang, J. Z. H.; Mei, Y.*; He, X.*, An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins, Journal of Chemical Physics, 139, 214104 (2013)
    DOI: 
    10.1063/1.4833678

    43. Lu, X. L.; Zeng, J.; Gao, Y.; Zhang, J. Z. H.; Zhang, D. W.; Mei, Y.*, The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: A replica exchange molecular dynamics study, Journal of Molecular Modeling, 19, 4897-4908 (2013)
    DOI: 
    10.1007/s00894-013-1985-7

    42. Zeng, J.; Jia, X. Y.; Zhang, J. Z. H.; Mei, Y.*, The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect, Journal of Computational Chemistry, 34, 2677-2686 (2013)
    DOI: 
    10.1002/jcc.23421

    41. Guo, M.; Mei, Y.*, Equilibrium and Folding Simulations of NS4B H2 in pure water and water/2,2,2-Trifluoroethanol mixed solvent: Examination of solvation models, Journal of Molecular Modeling, 19, 3931-3939 (2013)
    DOI: 
    10.1007/s00894-013-1933-6

    40. Gao, Y.; Lu, X. L.; Duan, L. L., Zhang, D. W.; Mei, Y.*; Zhang, J. Z. H.*, Direct folding simulation of a long helix in explicit water, Applied Physics Letters, 102, 193706 (2013)
    DOI: 
    10.1063/1.4807145

    39. Li, Y. X.; Gao, Y.; Zhang, X. Q.; Wang, X. Y.; Mou, L. R.; Duan, L. L.; He, X.*; Mei, Y.*; Zhang, J. Z. H.*, A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation, Journal of Molecular Modeling, 29, 3647-3657 (2013)
    DOI: 
    10.1007/s00894-013-1879-8

    38. Duan, L. L.; Zhu, T.; Mei, Y.*; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H.*; An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins, Journal of Molecular Modeling, 19, 2605-2612 (2013)
    DOI: 
    10.1007/s00894-013-1798-8

    37. Jia, X. Y.; Zhang, J. Z. H.*; Mei, Y.*, Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent, Journal of Molecular Modeling, 19, 2355–2361 (2013)
    DOI: 
    10.1007/s00894-013-1776-1

    36. Zeng, J.; Duan, L. L.; Zhang, J. Z. H.; Mei, Y.*, A numerically stable restrained electrostatic potential charge fitting method, Journal of Computational Chemistry, 34, 847-853 (2013)
    DOI: 
    10.1002/jcc.23208

    35. Ren, S.; Zeng, J.; Mei, Y.; Zhang, J. Z. H.; Yan, S. F.; Fei, J.; Chen, L.*, Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors, Drug Metabolism and Disposition, 41, 60-71 (2013)
    DOI: 
    10.1124/dmd.112.048264

    34. Xu, Z. J.; Lazim, R.; Mei, Y.; Zhang, D. W.*, Stability of the β-structure in prion protein: A molecular dynamics study based on polarized force field, Chemical Physics Letters‚ 539-540, 239-244 (2012)
    DOI: 
    10.1016/j.cplett.2012.05.025

    33. Mei, Y; He, X; Ji, C.G.; Zhang, D.W.; Zhang, J.Z.H.*, A fragmentation approach to quantum calculation of large molecular systems, Progress in Chemistry, 24, 1058 (2012)
    DOI: N/A

    32. Xu, Z. J.; Lazim, R.; Sun, T. D.; Mei, Y.; Zhang, D. W., Solvent effect on the folding dynamics and structure of E6ap characterized from ab initio protein folding simulations, Journal of Chemical Physics, 136, 135102 (2012)
    DOI: 
    10.1063/1.3698164

    31. Mei, Y.*; Li, Y. L.; Zeng, J.; Zhang, J. Z. H.*, Electrostatic polarization is critical for the strong binding in streptavidin-biotin system, Journal of Computational Chemistry,33, 1374 (2012)
    DOI: 
    10.1002/jcc.22970

    30. Duan, L. L.; Gao, Y.; Mei, Y.*; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H.*, Folding of helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water, Journal of Physical Chemistry B, 116, 3430 (2012)
    DOI: 
    10.1021/jp212516g

    29. Gao, Y.; Guo, M.; Mei, Y.; Zhang, J. Z. H.*, Protein-water hydrogen bonds are stabilized by electrostatic polarization, Molecular Physics, 110, 595 (2012)
    DOI: 
    10.1080/00268976.2012.668965

    28. Mei, Y.*; Wei, C. Y.; Yip, Y. M.; Ho, C. Y.; Zhang, J. Z. H., Zhang, D. W.*, Folding and thermodynamic studies of Trp-cage based on polarized force field, Theoretical Chemistry Accounts, 131, 1168 (2012)
    DOI: 
    10.1007/s00214-012-1168-0

    27. Lazim, R.; Mei, Y.*; Zhang, D. W.*, Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein, Journal of Molecular Modeling, 18, 1087 (2012)
    DOI: 
    10.1007/s00894-011-1147-8

    26. Gao, Y; Lu, X. L.; Duan, L. L.; Zhang, J. Z. H*, Mei, Y.*, Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix, Journal of Physical Chemistry B, 116, 549 (2012)
    DOI: 
    10.1021/jp208953x

    25. Mei, Y.*; Zhang, D. W.*; Duan, L. L.; Zhang, Q. G.; Zhang, J. Z. H.*, Folding of EK peptide and its dependence on salt concentration and pH: A computational study, Science China-Chemistry, 54, 1974 (2011)
    DOI: 
    10.1007/s11426-011-4399-3

    24. Li, Y. L.; Mei, Y.*; Zhang, D. W.; Xie, D. Q.; Zhang, J. Z. H.*, Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization, Journal of Physical Chemistry B, 115, 10154 (2011)
    DOI: 
    10.1021/jp203505v

    23. Wei‚ C. Y.; Tung‚ D.; Yip Y. M.; Mei‚ Y.*; Zhang‚ D. W.*‚ Communications: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants‚ Journal of Chemical Physics‚ 134‚ 171101 (2011)
    DOI: 
    10.1063/1.3581888

    22. Wei‚ C. Y.; Mei‚ Y.; Zhang‚ D. W.*‚ Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields‚ Chemical Physics Letters‚ 495‚ 121 (2010)
    DOI: 
    10.1016/j.cplett.2010.06.048

    21. Xu‚ Z. J.; Mei‚ Y.; Duan‚ L. L.; Zhang‚ D. W.*‚ Hydrogen bonds rebuilt by polarized protein-specific charges‚ Chemical Physics Letters‚ 495‚ 151-154 (2010)
    DOI: 
    10.1016/j.cplett.2010.06.073

    20. Wei‚ C. Y.; Liu‚ Z. Y.; Zhang‚ D. W.; Mei‚ Y.‚ Docking of raltegravir to HIV-1 integrase structure ensemble‚ Journal of Theoretical & Computational Chemistry‚ 9‚ 1053 (2010)
    DOI: 
    10.1142/s0219633610006201

    19. Duan‚ L. L.; Mei‚ Y.*; Li‚ Y. L.; Zhang‚ Q. G.; Zhang‚ J. Z. H.*‚ Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models‚ Science China-Chemistry‚ 53‚ 196-201 (2010)
    DOI: 
    10.1007/s11426-009-0196-7

    18. Duan‚ L. L.; Mei‚ Y.*; Zhang‚ D. W.; Zhang‚ Q. G.; Zhang‚ J. Z. H.*‚ Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds‚ Journal of the American Chemical Society‚ 132‚ 11159-11164 (2010)
    DOI: 
    10.1021/ja102735g

    17. Tong‚ Y.; Mei‚ Y.*; Li‚ Y. L.; Ji‚ C. G.; Zhang‚ J. Z. H.*‚ Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding‚ Journal of the American Chemical Society‚ 132‚ 5137-5142 (2010)
    DOI: 
    10.1021/ja909575j

    16. Lu‚ Y. P.; Mei‚ Y.; Zhang‚ J. Z. H.; Zhang‚ D. W.*‚ Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase‚ Journal of Chemical Physics‚ 132, 131101 (2010)
    DOI: 
    10.1063/1.3360769

    15. Duan‚ L. L.; Mei‚ Y.; Zhang‚ Q. G.; Zhang‚ J. Z. H.*‚ Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization‚ Journal of Chemical Physics‚ 130‚ 115102 (2009)
    DOI: 
    10.1063/1.3089723

    14. Mei‚ Y.; Zhang‚ J. Z. H.*‚ Numerical stabilities in fitting atomic charges to electric field and electrostatic potential‚ Journal of Theoretical & Computational Chemistry‚ 8‚ 925-942 (2009)
    DOI: 
    10.1142/s0219633609005295

    13. Tong‚ Y.; Mei‚ Y.; Zhang‚ J. Z. H.*; Duan‚ L. L.; Zhang‚ Q. G.‚ Quantum calculation of protein solvation and protein-ligand binding free energy for HIV-1 protease/water complex‚ Journal of Theoretical & Computational Chemistry‚ 8‚ 1265-1279 (2009)
    DOI: 
    10.1142/s0219633609005313

    12. Tong‚ Y.; Ji‚ C. G.; Mei‚ Y.; Zhang‚ J. Z. H.*‚ Simulation of NMR data reveals that proteins´ local structures are stabilized by electronic polarization‚ Journal of the American Chemical Society‚ 131‚ 8636-8641 (2009)
    DOI: 
    10.1021/ja901650r

    11. Li‚ Y. L.; Han‚ L.; Mei‚ Y.; Zhang‚ J. Z. H.*‚ Time-dependent density functional theory study of absorption spectra of metallocenes‚ Chemical Physics Letters‚ 482‚ 217-222 (2009)
    DOI: 
    10.1016/j.cplett.2009.10.026

    10. Ji‚ C. G.; Mei‚ Y.; Zhang‚ J. Z. H.*‚ Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pK(a) shifts for Asp(26)/Asp(20) in thioredoxin‚ Biophysical Journal‚ 95‚ 1080-1088 (2008)
    DOI: 
    10.1529/biophysj.108.131110

    9. Ding‚ Y.; Mei‚ Y.; Zhang‚ J. Z. H.*‚ Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding‚ Journal of Physical Chemistry B‚ 112‚ 11396-11401 (2008)
    DOI: 
    10.1021/jp8015886

    8. Ding‚ Y.; Mei‚ Y.; Zhang‚ J. Z. H.; Tao‚ F.-M.‚ Efficient bond function basis set for pi-pi interaction energies‚ Journal of Computational Chemistry‚ 29‚ 275-279 (2008)
    DOI: 
    10.1002/jcc.20788

    7. Wu‚ E. L.; Mei‚ Y.; Han‚ K. L.*; Zhang‚ J. Z. H.*‚ Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin‚ Biophysical Journal‚ 92‚ 4244 (2007)
    DOI: 
    10.1529/biophysj.106.099150

    6. Duan‚ L. L.; Tong‚ Y.; Mei‚ Y.; Zhang‚ Q. G.; Zhang‚ J. Z. H.*‚ Quantum study of HIV-1 protease-bridge water interaction‚ Journal of Chemical Physics‚ 127‚ 145101 (2007)
    DOI: 
    10.1063/1.2770720

    5. Mei‚ Y.; Ji‚ C. G.; Zhang‚ J. Z. H.*‚ A new quantum method for electrostatic solvation energy of protein‚ Journal of Chemical Physics‚ 125‚ 094906 (2006)
    DOI: 
    10.1063/1.2345201

    4. Mei‚ Y.; Wu‚ E. L.; Han‚ K. L.; Zhang‚ J. Z. H.‚ Treating hydrogen bonding in ab initio calculation of biopolymers‚ International Journal of Quantum Chemistry‚ 106‚ 1267-1276 (2006)
    DOI: 
    10.1002/qua.20875

    3. He‚ X.; Mei‚ Y.; Xiang‚ Y.; Zhang‚ D. W.; Zhang‚ J. Z. H.*‚ Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations‚ Proteins-Structure Function and Bioinformatics‚ 61‚ 423-432 (2005)
    DOI: 
    10.1002/prot.20578

    2. Mei‚ Y.; He‚ X.; Xiang‚ Y.; Zhang‚ D. W.; Zhang‚ J. Z. H.*‚ Quantum study of mutational effect in binding of efavirenz to HIV-1 RT‚ Proteins-Structure Function and Bioinformatics‚ 59‚ 489-495 (2005)
    DOI: 
    10.1002/prot.20455

    1. Mei‚ Y.; Zhang‚ D. W.; Zhang‚ J. Z. H.*‚ New method for direct linear-scaling calculation of electron density of proteins‚ Journal of Physical Chemistry A‚ 109‚ 2-5 (2005)
    DOI: 
    10.1021/jp045109y


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