All Faculty and Research Staff Publications

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2007
Ma L, Cui Q. Activation mechanism of a signaling protein at atomic resolution from advanced computations. Journal of the American Chemical Society. 2007 ;129:10261-10268.
Xu D, Guo H, Cui Q. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies. Journal of Physical Chemistry A. 2007 ;111:5630-5636.
Cai Z-L, Lopez P, Reimers JR, Cui Q, Elstner M. Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules. Journal of Physical Chemistry A. 2007 ;111:5743-5750.
Zhu X, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-mixed peptides. I. QM and QM/MM models. Journal of Chemical Theory and Computation. 2007 ;3:1538-1549.
Riccardi D, Cui Q. pK(a) analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "Multiscale" QM/MM simulations and mechanistic implications. Journal of Physical Chemistry A. 2007 ;111:5703-5711.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data. Structure. 2007 ;15:169-177.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data (vol 15, pg 169, 2007). Structure. 2007 ;15:637-637.
Nam K, Cui Q, Gao J, York DM. Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms. Journal of Chemical Theory and Computation. 2007 ;3:486-504.
Kissounko DA, Hoerter JM, Guzei IA, Cui Q, Gellman SH, Stahl SS. Ti-IV-mediated reactions between primary amines and secondary carboxamides: Amidine formation versus transamidation. Journal of the American Chemical Society. 2007 ;129:1776-1783.
Yu H, Cui Q. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding. Journal of Chemical Physics. 2007 ;127.
2006
Formaneck MS, Ma L, Cui Q. Effects of temperature and salt concentration on the structural stability of human lymphotactin: Insights from molecular simulations. Journal of the American Chemical Society. 2006 ;128:9506.
Van Wynsberghe AW, Cui Q. Interpreting correlated motions using normal mode analysis. Structure. 2006 ;14:1647.
Li G, Van Wynsberghe A, Demerdash ONA, Cui Q. Normal mode analysis of macromolecules: from enzyme active sites to molecular machines. Normal Mode Analysis. 2006 :65-89, 4 plates.
Kondrashov DA, Cui Q, Phillips GN. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data. Biophysical Journal. 2006 ;91:2760-2767.
Riccardi D, Koenig P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society. 2006 ;128:16302-16311.
Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: A prokaryotic protein involved in Fe(II) trafficking. Proteins Structure Function & Bioinformatics. 2006 ;62:578-586.
Ma L, Cui Q. The temperature dependence of salt-protein association is sequence specific. Biochemistry. 2006 ;45:14466.
Cui Q. Theoretical analysis of mechanochemical coupling in the biomolecular motor myosin. Modelling Molecular Structure and Reactivity in Biological Systems. 2006 :66-75.
Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theoretical Chemistry Accounts. 2006 ;116:51.
Konig PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, Cui Q. Toward theoretical analyis of long-range proton transfer kinetics in biomolecular pumps [Review]. Journal of Physical Chemistry A. 2006 ;110:548-563.
Formaneck MS, Cui Q. The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). Journal of Computational Chemistry. 2006 ;27:1923.
2005
Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Physical Chemistry Chemical Physics. 2005 ;7:3070-3079.
Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal. 2005 ;89:2939-2949.
Konig PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method [Review]. Journal of Physical Chemistry B. 2005 ;109:9082-9095.
Li GH, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. Journal of Molecular Graphics and Modelling. 2005 ;24:82-93.
Casey CP, Johnson JB, Singer SW, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: Study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. Journal of the American Chemical Society. 2005 ;127:3100-3109.
Guo H, Lipscomb WN, Cui Q, Karplus M. Molecular dynamics simulations of yeast chorismate mutase: substrate conformational transitions and enzymatic catalysis. NATO Sci. Ser., Ser. I. 2005 ;364:63-74.
Riccardi D, Schaefer P, Cui Q. pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols [Review]. Journal of Physical Chemistry B. 2005 ;109:17715-17733.
Casey CP, Bikzhanova GA, Cui Q, Guzei IA. Reduction of Imines by hydroxycyclopentadienyl ruthenium hydride: Intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. Journal of the American Chemical Society. 2005 ;127:14062-14071.
Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules - art. no. 014905. Journal of Chemical Physics. 2005 ;123:14905.
2003
Formaneck MS, Li GH, Zhang XD, Cui Q. Calculating accurate redox potentials in enzymes with a combined QM/MM free energy perturbation approach. Journal of Theoretical and Computational Chemistry. 2003 ;1:53-67.
Cui Q, Karplus M. Catalysis and specificity in enzymes: A study of triosephosphate isomerase and comparison with methyl glyoxal synthase [Review]. Protein Simulations. 2003 ;66:315-+.
Li GH, Zhang XD, Cui Q. Free energy perturbation calculations with combined QM/MM Potentials complications, simplifications, and applications to redox potential calculations. Journal of Physical Chemistry B. 2003 ;107:8643-8653.
Smedarchina Z, Siebrand W, Fernandez-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: A direct dynamics study of an active-site model of carbonic anhydrase. Journal of the American Chemical Society. 2003 ;125:243-251.
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F-1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 2003 ;100:874-879.
Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis [Review]. Journal of Computational Chemistry. 2003 ;24:565-581.
Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. Journal of Physical Chemistry B. 2003 ;107:14521-14528.
Cui Q, Karplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. Journal of Physical Chemistry B. 2003 ;107:1071-1078.
Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angewandte Chemie-International Edition. 2003 ;42:1508-1511.
Li GH, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM simulations. Journal of the American Chemical Society. 2003 ;125:15028-15038.

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