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Yingkai Zhang

Professor of Chemistry

    1993 …2019
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    Research Output 1993 2019

    • 90 Article
    • 2 Chapter (peer-reviewed)
    • 1 Chapter
    • 1 Comment/debate
    2009

    Born - Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4

    Ke, Z., Wang, S., Xie, D. & Zhang, Y., Dec 31 2009, In : Journal of Physical Chemistry B. 113, 52, p. 16705-16710 6 p.

    Research output: Contribution to journalArticle

    Arginine
    hydrolysis
    Molecular dynamics
    Hydrolysis
    molecular dynamics
    Electron energy levels
    Charge transfer
    Decomposition
    decomposition
    Dimers

    Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain

    Zhenyu, L., Lai, J. & Zhang, Y., Oct 21 2009, In : Journal of the American Chemical Society. 131, 41, p. 14928-14931 4 p.

    Research output: Contribution to journalArticle

    Histones
    Proteins
    Methylation
    Free energy
    Lysine

    Increasing the time step with mass scaling in born-oppenheimer ab Initio QM/MM molecular dynamics simulations

    Zheng, H., Wang, S. & Zhang, Y., Dec 2009, In : Journal of Computational Chemistry. 30, 16, p. 2706-2711 6 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Free energy
    Molecular dynamics
    Scaling
    MD Simulation

    Introducing sampling entropy in repository based adaptive umbrella sampling

    Zheng, H. & Zhang, Y., 2009, In : Journal of Chemical Physics. 131, 21, 214105.

    Research output: Contribution to journalArticle

    Entropy
    sampling
    entropy
    Sampling
    Free energy
    DNA-Directed DNA Polymerase
    Water
    Protons
    Phosphoranes
    Phosphates

    Reaction pathway and free-energy barrier for reactivation of dimethylphosphoryl-inhibited human acetylcholinesterase

    Liu, J., Zhang, Y. & Zhan, C. G., Dec 17 2009, In : Journal of Physical Chemistry B. 113, 50, p. 16225-16236 12 p.

    Research output: Contribution to journalArticle

    Energy barriers
    Acetylcholinesterase
    Free energy
    free energy
    Amino Acids

    Side chain specificity of ADP-ribosylation by a sirtuin

    Fahie, K., Hu, P., Swatkoski, S., Cotter, R. J., Zhang, Y. & Wolberger, C., Dec 2009, In : FEBS Journal. 276, 23, p. 7159-7176 18 p.

    Research output: Contribution to journalArticle

    Adenosine Diphosphate
    Trypanosoma brucei brucei
    Adenosine Diphosphate Ribose
    Arginine
    Proteins
    2008
    Molecular Dynamics Simulation
    Mechanics
    Free energy
    History
    sampling
    Niacinamide
    Molecular Dynamics Simulation
    Molecular dynamics
    Enzymes
    Computer simulation
    Histone-Lysine N-Methyltransferase
    Methylation
    Methyltransferases
    Molecular Dynamics Simulation
    Lysine
    Chlorine
    Molecular dynamics
    Chemical reactions
    chemical reactions
    molecular dynamics
    2007
    Histone-Lysine N-Methyltransferase
    lysine
    Catalysis
    catalysis
    Molecular dynamics

    A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV

    Wang, L., Yu, X., Hu, P., Broyde, S. & Zhang, Y., Apr 18 2007, In : Journal of the American Chemical Society. 129, 15, p. 4731-4737 7 p.

    Research output: Contribution to journalArticle

    Sulfolobus solfataricus
    DNA Polymerase beta
    DNA
    Water
    Substrates

    Catalytic mechanism and metal specificity of bacterial peptide deformylase: A density functional theory QM/MM study

    Xiao, C. & Zhang, Y., Jun 7 2007, In : Journal of Physical Chemistry B. 111, 22, p. 6229-6235 7 p.

    Research output: Contribution to journalArticle

    peptide deformylase
    Peptides
    peptides
    Density functional theory
    Metals
    Carbon
    valence
    Atoms
    Electrons
    carbon

    Tuning the membrane selectivity of antimicrobial peptides by using multivalent design

    Liu, Z., Young, A. W., Hu, P., Rice, A. J., Zhou, C., Zhang, Y. & Kallenbach, N. R., Nov 23 2007, In : ChemBioChem. 8, 17, p. 2063-2065 3 p.

    Research output: Contribution to journalArticle

    Fluoresceins
    Dendrimers
    Molecular Models
    Drug Design
    Cell membranes
    2006
    Histone-Lysine N-Methyltransferase
    Molecular Dynamics Simulation
    Histones
    Methylation
    Free energy

    Geometric preferences in iron(II) and zinc(II) model complexes of peptide deformylase

    Karambelkar, V. V., Xiao, C., Zhang, Y., Narducci Sarjeant, A. A. & Goldberg, D. P., Feb 20 2006, In : Inorganic Chemistry. 45, 4, p. 1409-1411 3 p.

    Research output: Contribution to journalArticle

    formic acid
    peptide deformylase
    formates
    peptides
    Metal ions

    How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study

    Cheng, Y., Zhang, Y. & McCammon, J. A., Apr 2006, In : Protein Science. 15, 4, p. 672-683 12 p.

    Research output: Contribution to journalArticle

    Phosphorylation
    Cyclic AMP-Dependent Protein Kinases
    Catalyst activity
    Catalytic Domain
    Theoretical Models

    Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

    Zhang, Y., Aug 2006, In : Theoretical Chemistry Accounts. 116, 1-3, p. 43-50 8 p.

    Research output: Contribution to journalArticle

    enzymes
    Enzymes
    Free energy
    free energy
    methodology

    Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein

    Corminboeuf, C., Hu, P., Tuckerman, M. & Zhang, Y., Apr 12 2006, In : Journal of the American Chemical Society. 128, 14, p. 4530-4531 2 p.

    Research output: Contribution to journalArticle

    Histone Deacetylases
    Density functional theory
    Proteins
    Zinc
    Protonation
    2005

    An efficient approach for ab initio energy calculation of biopolymers

    Chen, X., Zhang, Y. & Zhang, J., May 8 2005, In : Journal of Chemical Physics. 122, 18, 184105.

    Research output: Contribution to journalArticle

    Biopolymers
    biopolymers
    Fractionation
    caps
    fractionation

    How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab Initio QM/MM study

    Cheng, Y., Zhang, Y. & McCammon, J. A., Feb 9 2005, In : Journal of the American Chemical Society. 127, 5, p. 1553-1562 10 p.

    Research output: Contribution to journalArticle

    Phosphorylation
    Cyclic AMP-Dependent Protein Kinases
    Protein Kinases
    Catalytic Domain
    Ions
    Atoms
    valence
    atoms
    Electrons
    proteins

    Molecular docking of balanol to dynamics snapshots of protein kinase A

    Wong, C. F., Kua, J., Zhang, Y., Straatsma, T. P. & McCammon, J. A., Dec 1 2005, In : Proteins: Structure, Function and Genetics. 61, 4, p. 850-858 9 p.

    Research output: Contribution to journalArticle

    Cyclic AMP-Dependent Protein Kinases
    Ligands
    Molecular Dynamics Simulation
    Conformations
    Molecular dynamics
    2004

    An efficient linear scaling method for ab initio calculation of electron density of proteins

    Gao, A. M., Zhang, D. W., Zhang, J. & Zhang, Y., Aug 21 2004, In : Chemical Physics Letters. 394, 4-6, p. 293-297 5 p.

    Research output: Contribution to journalArticle

    caps
    Carrier concentration
    proteins
    scaling
    Fractionation
    2003

    Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

    Cisneros, G. A., Liu, H., Zhang, Y. & Yang, W., Aug 27 2003, In : Journal of the American Chemical Society. 125, 34, p. 10384-10393 10 p.

    Research output: Contribution to journalArticle

    Hydrogen
    Carbon
    Acids
    Energy barriers
    Substrates

    Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies

    Zhang, Y., Kua, J. & McCammon, J. A., May 8 2003, In : Journal of Physical Chemistry B. 107, 18, p. 4459-4463 5 p.

    Research output: Contribution to journalArticle

    Energy barriers
    enzymes
    Enzymes
    Conformations
    Acetylcholinesterase

    Studying the affinity and kinetics of molecular association with molecular-dynamics simulation

    Zhang, Y. & McCammon, J. A., Jan 22 2003, In : Journal of Chemical Physics. 118, 4, p. 1821-1827 7 p.

    Research output: Contribution to journalArticle

    affinity
    Molecular dynamics
    Association reactions
    molecular dynamics
    Kinetics

    Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach

    Kua, J., Zhang, Y., Eslami, A. C., Butler, J. R. & McCammon, J. A., Dec 2003, In : Protein Science. 12, 12, p. 2675-2684 10 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Acetylcholinesterase
    Acetylcholine
    Molecular dynamics
    Static Electricity
    2002

    Ab initio qm/mm and free energy calculations of enzyme reactions

    Zhang, Y., Liu, H. & Yang, W., 2002, Computational methods for macromolecules: Challenges and applications. Schlick, T. & Gan, H. H. (eds.). Springer Verlag, p. 332-354

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

    Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: An ab initio QM/MM study

    Zhang, Y., Kua, J. & McCammon, J. A., Sep 4 2002, In : Journal of the American Chemical Society. 124, 35, p. 10572-10577 6 p.

    Research output: Contribution to journalArticle

    Acetylcholinesterase
    Catalysis
    Hydrogen
    Hydrogen bonds
    Oxygen

    Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

    Kua, J., Zhang, Y. & McCammon, J. A., Jul 17 2002, In : Journal of the American Chemical Society. 124, 28, p. 8260-8267 8 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Acetylcholinesterase
    Acetylcholine
    Molecular dynamics
    Enzymes
    2000

    Degenerate Ground States and a Fractional Number of Electrons in Density and Reduced Density Matrix Functional Theory

    Yang, W., Zhang, Y. & Ayers, P. W., May 29 2000, In : Physical Review Letters. 84, 22, p. 5172-5175 4 p.

    Research output: Contribution to journalArticle

    ground state
    electrons
    energy
    functionals
    integers

    Density functional study of a weakly hydrogen-bonded benzene-ammonia complex: The importance of the exchange functional

    Enkvist, C., Zhang, Y. & Yang, W., Sep 2000, In : International Journal of Quantum Chemistry. 79, 5, p. 325-329 5 p.

    Research output: Contribution to journalArticle

    Benzene
    Ammonia
    ammonia
    Hydrogen
    benzene
    Potential energy surfaces
    Free energy
    enzymes
    potential energy
    free energy

    How is the active site of enolase organized to catalyze two different reaction steps?

    Liu, H., Zhang, Y. & Yang, W., Jul 19 2000, In : Journal of the American Chemical Society. 122, 28, p. 6560-6570 11 p.

    Research output: Contribution to journalArticle

    Phosphopyruvate Hydratase
    Cations
    Catalytic Domain
    Positive ions
    Metals

    Perspective on "Density-functional theory for fractional particle number: Derivative discontinuities of the energy"

    Zhang, Y. & Yang, W., Feb 2000, In : Theoretical Chemistry Accounts. 103, 3-4, p. 346-348 3 p.

    Research output: Contribution to journalArticle

    Density functional theory
    discontinuity
    density functional theory
    Derivatives
    integers
    1999

    A pseudobond approach to combining quantum mechanical and molecular mechanical methods

    Zhang, Y., Lee, T. S. & Yang, W., 1999, In : Journal of Chemical Physics. 110, 1, p. 46-54 9 p.

    Research output: Contribution to journalArticle

    Atoms
    atoms
    Potential energy surfaces
    Molecules
    Covalent bonds
    1998
    functionals
    dissociation
    Electrons
    electrons
    interactions

    Comment on "Generalized gradient approximation made simple"

    Zhang, Y. & Yang, W., 1998, In : Physical Review Letters. 80, p. 890

    Research output: Contribution to journalComment/debate

    1997

    Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional

    Zhang, Y., Pan, W. & Yang, W., Nov 15 1997, In : Journal of Chemical Physics. 107, 19, p. 7921-7925 5 p.

    Research output: Contribution to journalArticle

    diatomic molecules
    Noble Gases
    Local density approximation
    gradients
    Molecules
    1993

    Application of the faraday effect in chemistry

    Zhang, Y., Wang, G. & Jiang, Y., 1993, In : Journal of Nanjing University (Natural Science Edition). 29, p. 400-406

    Research output: Contribution to journalArticle