研究领域

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

近期论文

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, accepted
DOI: 10.1021/acs.jctc.6b01125
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, accepted
DOI: 10.1021/acs.jcim.6b00589
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
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
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
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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