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Pan, X.; Snyder, R.; Wang, J.-N.; Lander, C.; Wickizer, C.; Van, R.; Chesney, A.; Xue, Y.; Mao, Y.; Mei, Y.; Pu, J.; Shao, Y., Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models, Journal of Computational Chemistry, online available
DOI: 10.1002/jcc.27269
Guo, J.; Xue, Y.; Zhao, C.; Zhao, J.; Gao, Z.; Mei, Y.*; Song, Y.-Y.*, Integrated separation-electrochemical detection device based on wood column for online identification of enantiomer, Nano Research, accepted
DOI:10.1007/s12274-023-6000-8
Jin, P.; Wang, J.-N.; Wang, X.; Jia, M.; Pan, H.; Mei, Y.*; Chen, J.*; Tracking early stage of triplet induced photodamage in DNA dimer and oligomer containing 5-methylcytosine, Journal of Physical Chemistry B, 127, 6878-6886 (2023)
DOI: 10.1021/acs.jpcb.3c02454
Wang, J.-N.; Xue, Y.; Li, P.; Pan, X.; Wang, M.; Shao, Y.*; Mo, Y.*; Mei, Y.*; Perspective: Reference-potential methods for the study of thermodynamic properties in chemical processes: Theory, applications, and pitfalls, Journal of Physical Chemistry Letters, 14, 4866–4875 (2023)
DOI: 10.1021/acs.jpclett.3c00671
Yao, S.; Van, R.; Pan, X.; Park, J. H.; Mao, Y.*; Pu, J.*; Mei, Y.*; Shao, Y.*; Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations, RSC Advances, 13, 4565-4577 (2023)
DOI: 10.1039/d2ra08180f
Luo, F.; Zhao, J.; Liu, S.; Xue, Y.; Tang, D.; Yang, J.; Mei, Y.; Li, G.*; Xie, Y.*, Ursolic acid augments the chemosensitivity of drug-resistant breast cancer cells to doxorubicin by AMPK-mediated mitochondrial dysfunction, Biochemical Pharmacology, 205, 115278 (2022)
DOI: 10.1016/j.bcp.2022.115278
Xu, J.; Xue, Y.; Jian, X.; Zhao, Y.; Dai, Z.; Xu, J.; Gao, Z.; Mei, Y.*; Song, Y.-Y.*, Understanding of chiral site-dependent enantioselective identification on plasmon-free semiconductor based SERS substrate, Chemical Science, 13, 6550-6557 (2022)
DOI: 10.1039/D2SC01938H
Liu, F.*; Ma, S.; Lu, Z.; Nangia, A.; Duan, M.; Yu, Y.; Xu, G.; Mei, Y.; Bietti, M.*; Houk, K. N.*, Hydrogen abstraction by alkoxyl radicals: Computational studies of thermodynamic and polarity effects on reactivities and selectivities, Journal of the American Chemical Society, 144, 15, 6802–6812 (2022) (JACS Spotlights)
DOI: 10.1021/jacs.2c00389
Yang, L.; Feng, J.; Wang, J.-N.; Gao, Z.; Xu, J.*; Mei, Y.*; Song, Y.-Y.*,Engineering large-scaled electrochromic semiconductor films as reproductive SERS substrates for operando investigation at the solid/liquid interfaces, Chinese Chemical Letters, 33, 5169-5173 (2022)
DOI: 10.1016/j.cclet.2022.03.011
Qu, K.; Xu, J.; Xue, Y.; Guo, J.; Gao, Z.; Song, Y.-Y.*; Mei, Y.*, NIR light-driven Photothermal effect on homochiral Au/TiO2 nanotube arrays for enantioselective desorption, Analytical Chemistry, 94, 2, 588–592 (2022)
DOI: 10.1021/acs.analchem.1c04981
Xue, Y.; Wang, J.-N.; Hu, W.; Zheng, J.; Li, Y.; Pan, X.; Mo, Y.*, Shao, Y.; Wang L.*; Mei, Y.*, Affordable ab initio path integral for thermodynamic properties via molecular dynamics simulations using semiempirical reference potential, Journal of Physical Chemistry A, 125, 50, 10677–10685 (2021)
DOI: 10.1021/acs.jpca.1c07727
Jin, S.; Wang, J.-N.; Xue, Y.; Li, P.; Mei, Y.*, Study of the selectivity of Parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential method, Chinese Journal of Chemical Physics, online available (Part of Special Issue “John Z.H. Zhang Festschrift for celebrating his 60th birthday”)
DOI: 10.1063/1674-0068/cjcp2109176
Pan, X.; Yang, J.; Van, R.; Epifanovsky, E.; Ho, J.; Huang, J.; Pu, J.; Mei, Y.*; Nam, K.*; Shao, Y.*, Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions, Journal of Chemical Theory and Computation, 2021, 17, 9, 5745–5758
DOI: 10.1021/acs.jctc.1c00565
Huai, Z.; Tong, Z.; Mei, Y.; Mo, Y.*, A theoretical study of the spectral differences of the Fenna-Matthews-Olson protein from different species and their mutants, Journal of Physical Chemistry B, 125, 30, 8313--8324 (2021)
DOI: 10.1021/acs.jpcb.1c01686
Jia, X.*; Ge, H.; Mei, Y., Free energy change estimation: The divide and conquer MBAR method, Journal of Computational Chemistry, 42: 1204–1211 (2021)
DOI: 10.1002/jcc.26533
Wang, J.-N.; Liu, W.; Li, P.*, Mo, Y.*, Hu, W.; Zheng, J.; Pan, X.; Shao, Y.; Mei, Y.*, Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 4. Adaptive QM/MM, Journal of Chemical Theory and Computation, 17, 3, 1318–1325 (2021)
DOI: 10.1021/acs.jctc.0c01149
Hu, W.; Li, P.*; Wang, J.-N.; Xue, Y.; Mo, Y.*; Zheng, J.; 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. 3. Gaussian smoothing on density-of-states, Journal of Chemical Theory and Computation, 16, 11, 6814-6822 (2020)
DOI: 10.1021/acs.jctc.0c00794
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
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
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 Computation, 16, 587-600 (2020)
DOI: 10.1021/acs.jctc.9b00823
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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