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Lu XY, Cui Q. Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins. Journal of Physical Chemistry B. 2013;117:2005-2018. |
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Yoo J, Jackson MB, Cui Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores. Biophysical Journal. 2013;104:841-852. |
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Yoo J, Cui Q. Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association. Biophysical Journal. 2013;104:128-138. |
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Yoo J, Cui Q. Three-Dimensional Stress Field around a Membrane Protein: Atomistic and Coarse-Grained Simulation Analysis of Gramicidin A. Biophysical Journal. 2013;104:117-127. |
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Daily MD, Makowski L, Phillips GN, Cui Q. Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering. Chemical Physics. 2012;396:84-91. |
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Meuwly M, Cui Q. Protein functional dynamics: From femtoseconds to milliseconds Preface. Chemical Physics. 2012;396:1-2. |
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Xing YN, Nukaya M, Satyshur KA, Jiang L, Stanevich V, Korkmaz EN, et al. Identification of the Ah-Receptor Structural Determinants for Ligand Preferences. Toxicological Sciences. 2012;129:86-97. |
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Xia F, Rudack T, Cui Q, Kotting C, Gerwert K. Detailed Structure of the H2PO4--Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations. Journal of the American Chemical Society. 2012;134:20041-20044. |
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Hou GH, Zhu X, Elstner M, Cui Q. A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions. Journal of Chemical Theory and Computation. 2012;8:4293-4304. |
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Zienau J, Cui Q. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems. Journal of Physical Chemistry B. 2012;116:12522-12534. |
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Hou G, Zhu X, Elstner M, Cui Q. A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions. Journal of Chemical Theory and Computation. 2012;8:4293-4304. |
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Zienau J, Cui Q. Implementation of the solvent macromolecule boundary potential and application to model and realistic enzyme systems. J Phys Chem B. 2012;116(41):12522-34. |
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Clemens M, Phatak P, Cui Q, Bondar A-N, Elstner M. Role of Arg82 in the Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle. Journal of Physical Chemistry B. 2011;115:7129-7135. |
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Daily MD, Phillips, George N. J, Cui Q. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases. Plos Computational Biology. 2011;7. |
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Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water. Journal of Physical Chemistry B. 2011;115:6790-6805. |
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Goyal P, Ghosh N, Phatak P, Clemens M, Gaus M, Elstner M, et al. Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pK(a) and Infrared Spectra. Journal of the American Chemical Society. 2011;133:14981-14997. |
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Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and Formation of Surface Salt Bridges Are Coupled to DNA Binding by the Integration Host Factor: A Computational Analysis. Biochemistry. 2011;50:266-275. |
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Wu Y, Ma L, Cheley S, Bayley H, Cui Q, Chapman ER. Permeation of Styryl Dyes through Nanometer-Scale Pores in Membranes. Biochemistry. 2011;50:7493-7502. |
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Wu Z, Cui Q, Yethiraj A. Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. Journal of Physical Chemistry Letters. 2011;2:1794-1798. |
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Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Force Field for Membrane-Peptide Simulations. Journal of Chemical Theory and Computation. 2011;7:3793-3802. |
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Yang S, Cui Q. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase. Biophysical Journal. 2011;101:61-69. |
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Yang Y, Mkhonto D, Cui Q, Sahai N. Theoretical Study of Bone Sialoprotein in Bone Biomineralization. Cells Tissues Organs. 2011;194:182-187. |
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Yang W, Cui Q, Min D, Li H. Chapter 4 - QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments. In: Wheeler RA. Annual Reports in Computational Chemistry. Elsevier; 2010. p. 51 - 62. |
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Ma L, Pegram L, Record MT, Cui Q. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010;49:1954-1962. |
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Mondal J, Zhu X, Cui Q, Yethiraj A. Self-Assembly of beta-Peptides: Insight from the Pair and Many-Body Free Energy of Association. Journal of Physical Chemistry C. 2010;114:13551-13556. |
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Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent Interaction of beta-Peptides with Membranes. Journal of Physical Chemistry B. 2010;114:13585-13592. |
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Riccardi D, Yang S, Cui Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2010;1804:342-351. |
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Van Wynsberghe AW, Cui Q. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 2010;18:281-283. |
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Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. Journal of Physical Chemistry B. 2010;114:10524-10529. |
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Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for beta- and alpha/beta-Peptides. III. Molecular Mechanical Model for Acyclic beta-Amino Acids. Journal of Computational Chemistry. 2010;31:2063-2077. |
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Rao L, Cui Q, Xu X. Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator. Journal of the American Chemical Society. 2010;132:18092-18102. |
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Hou G, Zhu X, Cui Q. An Implicit Solvent Model for SCC-DFTB with Charge-Dependent Radii. Journal of Chemical Theory and Computation. 2010;6:2303-2314. |
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Daily MD, Jr. GPN, Cui Q. Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition. Journal of Molecular Biology. 2010;400:618 - 631. |
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Ma L, Pegram L, Record MT, Cui Q. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010;49:1954-1962. |
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Yang Y, Cui Q, Sahai N. How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations. Langmuir. 2010;26(12):9848-59. |
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Yoo J, Cui Q. Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculations. Biophys J. 2010;99(5):1529-38. |
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Riccardi D, Cui Q, Phillips GN. Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering. Biophys J. 2010;99(8):2616-25. |
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Ghosh N, Prat-Resina X, Gunner MR, Cui Q. Microscopic pK(a) Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model. Biochemistry. 2009;48:2468-2485. |
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Ma L, Yethiraj A, Chen X, Cui Q. A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability. Biophysical Journal. 2009;96:3543-3554. |
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Riccardi D, Cui Q, Phillips GN. Application of Elastic Network Models to Proteins in the Crystalline State. Biophysical Journal. 2009;96:464-475. |
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Tang Y, Chen X, Yoo J, Yethiraj A, Cui Q. Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli. Experimental Mechanics. 2009;49:35-46. |
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Yang Y, Cui Q. Does Water Relay Play an Important Role in Phosphoryl Transfer Reactions? Insights from Theoretical Study of a Model Reaction in Water and tert-Butanol. Journal of Physical Chemistry B. 2009;113:4930-4939. |
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Yang Y, Cui Q. The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition State. Journal of Physical Chemistry A. 2009;113:12439-12446. |
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Yoo J, Cui Q. Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations. Biophysical Journal. 2009;97:2267-2276. |
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Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30(10):1545-614. |
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Schwede T, Peitsch MC, Cui Q. Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales. World Scientific; 2008. |
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Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating mechanisms of mechanosensitive channels of large conductance, I: A continuum mechanics-based hierarchical framework. Biophysical Journal. 2008;95:563-580. |
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Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science. 2008;17:1295-1307. |
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Ghosh N, Cui Q. pK(a) of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. Journal of Physical Chemistry B. 2008;112:8387-8397. |
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Hoerter JM, Otte KM, Gellman SH, Cui Q, Stahl SS. Discovery and mechanistic study of Al-III-catalyzed transamidation of tertiary amides. Journal of the American Chemical Society. 2008;130:647-654. |
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Phatak P, Ghosh N, Yu HB, Cui Q, Elstner M. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:19672-19677. |
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Riccardi D, Koenig P, Guo H, Cui Q. Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry. 2008;47:2369-2378. |
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Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating mechanisms of mechanosensitive channels of large conductance, II: Systematic study of conformational transitions. Biophysical Journal. 2008;95:581-596. |
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Tang YY, Yoo J, Yethiraj A, Cui Q, Chen X. Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochemistry and Biophysics. 2008;52:1-18. |
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Yang Y, Yu H, Cui Q. Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. Journal of Molecular Biology. 2008;381:1407-1420. |
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Yang Y, Yu HB, York D, Elstner M, Cui Q. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization. Journal of Chemical Theory and Computation. 2008;4:2067-2084. |
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Yoo J, Cui Q. Does arginine remain protonated in the lipid membrane? Insights from microscopic pK(a) calculations. Biophysical Journal. 2008;94:L61-L63. |
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Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Peptides. II. Molecular Mechanical (MM) Model for a Cyclic β-Residue. The Journal of Physical Chemistry B [Internet]. 2008;112:5439-5448. Available from: http://pubs.acs.org/doi/abs/10.1021/jp077601y |
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Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating Mechanisms of Mechanosensitive Channels of Large Conductance, II: Systematic Study of Conformational Transitions. Biophysical Journal. 2008;95:581 - 596. |
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Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework. Biophysical Journal. 2008;95:563 - 580. |
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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. |
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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. |
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Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, George N. J. Protein structural variation in computational models and crystallographic data. Structure. 2007;15:169-177. |
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Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, George N. J. Protein structural variation in computational models and crystallographic data (vol 15, pg 169, 2007). Structure. 2007;15:637-637. |
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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. |
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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. |
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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. |
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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. |
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Yang Y, Cui Q. Interactions between phosphate and water in solution: A natural bond orbital based analysis in a QM/MM framework. Journal of Physical Chemistry B. 2007;111:3999-4002. |
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Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. Journal of Physical Chemistry A. 2007;111:10861-10873. |
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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. |
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Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. Plos Computational Biology. 2007;3:199-213. |
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Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Plos Computational Biology. 2007;3:214-230. |
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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. |
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Xu D, Guo H, Cui Q. Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies. J Am Chem Soc. 2007;129(35):10814-22. |
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Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A. 2007;111(42):10861-73. |
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Cui Q, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). Journal of Physical Chemistry B. 2006;110:548-563. |
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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. |
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Ma L, Cui Q. The temperature dependence of salt-protein association is sequence specific. Biochemistry. 2006;45:14466. |
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Riccardi D, Koenig P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, et al. "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. |
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Van Wynsberghe AW, Cui Q. Interpreting correlated motions using normal mode analysis. Structure. 2006;14:1647. |
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Konig PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, et al. Toward theoretical analyis of long-range proton transfer kinetics in biomolecular pumps [Review]. Journal of Physical Chemistry AJournal of Physical Chemistry A Molecules. 2006;110:548-563. |
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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. |
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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. |
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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 & BioinformaticsProteins. 2006;62:578-586. |
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Cui Q. Theoretical analysis of mechanochemical coupling in the biomolecular motor myosin. Modelling Molecular Structure and Reactivity in Biological Systems. 2006;:66-75. |
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Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theoretical Chemistry Accounts. 2006;116:51. |
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König PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, et al. Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A. 2006;110(2):548-63. |
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Formaneck MS, Ma L, Cui Q. Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins. 2006;63(4):846-67. |
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Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, et al. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B. 2006;110(13):6458-69. |
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Tang Y, Cao G, Chen X, Yoo J, Yethiraj A, Cui Q. A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J. 2006;91(4):1248-63. |
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Formaneck MS, Ma L, Cui Q. Effects of temperature and salt concentration on the structural stability of human lymphotactin: insights from molecular simulations. J Am Chem Soc. 2006;128(29):9506-17. |
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Kondrashov DA, Cui Q, Phillips GN. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J. 2006;91(8):2760-7. |
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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). J Comput Chem. 2006;27(16):1923-43. |
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Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal. 2005;89:2939-2949. |
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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. |
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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 BJournal of Physical Chemistry B. 2005;109:17715-17733. |
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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 BJournal of Physical Chemistry B. 2005;109:9082-9095. |
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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. |
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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. |
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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. J Am Chem Soc. 2005;127(9):3100-9. |
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Li G, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. J Mol Graph Model. 2005;24(2):82-93. |
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Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys. 2005;123(1):014905. |
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Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J. 2005;89(5):2939-49. |
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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. Phys Chem Chem Phys. 2005;7(16):3070-9. |
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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. J Am Chem Soc. 2005;127(40):14062-71. |
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König PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B. 2005;109(18):9082-95. |
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Xu DG, Guo H, Gao JL, Cui Q. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Chemical CommunicationsChemical Communications. 2004;:892-893. |
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Van Wynsberghe A, Li GH, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. BiochemistryBiochemistry. 2004;43:13083-13096. |
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Riccardi D, Li GH, Cui Q. Importance of van der Waals interactions in QM/MM Simulations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2004;108:6467-6478. |
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Li GH, Cui Q. Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2004;108:3342-3357. |
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Li GH, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: Myosin-II and Ca2+-ATPase [Review]. Biophysical Journal. 2004;86:743-763. |
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Li G, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase. Biophys J. 2004;86(2):743-63. |
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Cui Q, Li G, Ma J, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol. 2004;340(2):345-72. |
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Van Wynsberghe A, Li G, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 2004;43(41):13083-96. |
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Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, et al. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. J Am Chem Soc. 2004;126(42):13649-58. |
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Riccardi D, Li G, Cui Q. Importance of van der Waals Interactions in QM/MM Simulations. J Phys Chem B. 2004;108(20):6467-78. |
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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. |
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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. |
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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 BJournal of Physical Chemistry B. 2003;107:8643-8653. |
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Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2003;107:14521-14528. |
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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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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 EditionAngewandte Chemie-International Edition. 2003;42:1508-1511. |
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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. |
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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. |
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Cui Q, Karplus M. Catalysis and specificity in enzymes: A study of triosephosphate isomerase and comparison with methyl glyoxal synthase [Review]. Protein SimulationsProtein Simulations. 2003;66:315-+. |
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Cui Q, Karplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2003;107:1071-1078. |
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Li G, Zhang X, Cui Q. Free Energy Perturbation Calculations with Combined QM/MM Potentials Complications, Simplifications, and Applications to Redox Potential Calculations. The Journal of Physical Chemistry B. 2003;107:8643-8653. |
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Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proceedings of the National Academy of Sciences. 2003;100:874-879. |
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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. J Comput Chem. 2003;24:565-81. |
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Smedarchina Z, Siebrand W, Fernández-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II. J Am Chem Soc. 2003;125(1):243-51. |
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Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angew Chem Int Ed Engl. 2003;42(13):1508-11. |
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Li G, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc. 2003;125(49):15028-38. |
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Cui Q. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine. Journal of Chemical Physics. 2002;117:4720-4728. |
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Zhang XD, Harrison DHT, Cui Q. Functional Specificities of methylglyoxal synthase and triosephosphate isomerase: A combined QM/MM analysis. Journal of the American Chemical Society. 2002;124:14871-14878. |
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Ma JP, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F-1-ATPase. StructureStructure. 2002;10:921-931. |
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Li GH, Cui Q. A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase. Biophysical Journal. 2002;83:2457-2474. |
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Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: Verification of methodology and analysis of reaction mechanisms. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2002;106:1768-1798. |
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Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants. Journal of the American Chemical Society. 2002;124:3093-3124. |
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Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods. Journal of Chemical Physics. 2002;117:5617-5631. |
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Cui Q, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). Journal of Physical Chemistry BJournal of Physical Chemistry B. 2002;106:2721-2740. |
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Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods. The Journal of Chemical Physics. 2002;117:5617-5631. |
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Cui Q, Karplus M. {Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: a study of models and realistic systems}. J. Phys. Chem. B. 2002;106:7927–7947. |
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Cui Q, Elstner M, Karplus M. {A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (ladh)}. J. Phys. Chem. B. 2002;106:2721–2740. |
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Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc. 2002;124:3093-124. |
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Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: verification of methodology and analysis of reaction mechanisms. J. Phys. Chem. B. 2002;106:1768–1798. |
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Ma J, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure. 2002;10(7):921-31. |
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Li G, Cui Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J. 2002;83(5):2457-74. |
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Zhang X, Harrison DHT, Cui Q. Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. J Am Chem Soc. 2002;124(50):14871-8. |
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Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. Journal of Physical Chemistry B. 2001;105:569-585. |
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Cui Q, Karplus M. Triosephosphate isomerase: A theoretical comparison of alternative pathways. Journal of the American Chemical Society. 2001;123:2284-2290. |
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Guo H, Cui Q, Lipscomb WN, Karplus M. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism. Proceedings of the National Academy of Sciences of the United States of America. 2001;98:9032-9037. |
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Cui Q, Karplus M. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. Journal of Chemical Physics. 2000;112:1133-1149. |
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Cui Q, Karplus M. Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules. Journal of Physical Chemistry B. 2000;104:3721-3743. |
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Cui Q, Morokuma K. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited I. Ab initio study of the potential energy surfaces. Theoretical Chemistry Accounts. 1999;102:127-133. |
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Cui Q, Morokuma K, Bowman JM, Klippenstein SJ. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited. II. Nonadiabatic transition state theory and application. Journal of Chemical Physics. 1999;110:9469-9482. |
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Kaledin AL, Cui Q, Heaven MC, Morokuma K. Ab initio theoretical studies on photodissociation of HNCO upon S-1((1)A '')<- S-0((1)A(')) excitation: The role of internal conversion and intersystem crossing. Journal of Chemical Physics. 1999;111:5004-5016. |
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G. MD, Cui Q, Mats S, Keiji M. Theoretical Studies of the N2 Cleavage by Three-Coordinate Group 6 Complexes ML3. In: Transition State Modeling for Catalysis. 1998. p. 198-207. |
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Cui Q, Morokuma K. Ab initio molecular orbital studies on the structure, energies, and photodissociation of the electronic excited states of C2H. Journal of Chemical Physics. 1998;108:626-636. |
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Cui Q, Morokuma K. Ab initio study on the mechanism of C2H2+NH3 reaction: Efficient charge transfer and proton transfer processes competing with stable complex formation. Journal of Chemical Physics. 1998;108:4021-4030. |
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Cui Q, Morokuma K. Ab initio studies on the electronic excited states and photodissociation of O-3 anion. Journal of Chemical Physics. 1998;108:7684-7694. |
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Cui Q, Musaev DG, Morokuma K. Why do Pt(PR3)(2) complexes catalyze the alkyne diboration reaction, but their palladium analogues do not? A density functional study. Organometallics. 1998;17:742-751. |
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Cui Q, Musaev DG, Morokuma K. Density functional study on the mechanism of palladium(0)-catalyzed thioboration reaction of alkynes. Differences between Pd(0) and Pt(0) catalysts and between thioboration and diboration. Organometallics. 1998;17:1383-1392. |
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Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. I. Pt, Pd, Pt-2, and Pd-2. Journal of Chemical Physics. 1998;108:8418-8428. |
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Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. 2. Pd-3 and Pt-3. Journal of Physical Chemistry A. 1998;102:6373-6384. |
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Cui Q, Liu ZW, Morokuma K. Theoretical study on the mechanism CH4+C2H2+ reaction: Mode-enhancement effect. Journal of Chemical Physics. 1998;109:56-62. |
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Kaledin AL, Heaven MC, Lawrence WG, Cui Q, Stevens JE, Morokuma K. Ab initio molecular-orbital study of the trichlorine radical, Cl-3. Journal of Chemical Physics. 1998;108:2771-2783. |
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Morokuma K, Cui Q, Liu ZW. Potential-energy surfaces and their dynamic implications. Faraday Discussions. 1998;110:71-89. |
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Stevens JE, Cui Q, Morokuma K. An ab initio study of the dissociation of HNCO in the S-1 electronic state. Journal of Chemical Physics. 1998;108:1452-1458. |
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Stevens JE, Cui Q, Morokuma K. An ab initio investigation of spin-allowed and spin-forbidden pathways of the gas phase reactions of O(P-3)+C2H5I. Journal of Chemical Physics. 1998;108:1544-1551. |
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Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state .2. Mechanism involving triplet states. Chemical Physics Letters. 1997;272:319-327. |
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Cui Q, Morokuma K. Ab initio study of nonadiabatic interactions in the photodissociation of ketene. Journal of Chemical Physics. 1997;107:4951-4959. |
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Cui Q, Musaev DG, Morokuma K. Molecular orbital study of the mechanism of platinum(0)-catalyzed alkene and alkyne diboration reactions. Organometallics. 1997;16:1355-1364. |
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Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of the methoxy family CX(3)Y (X=H,F; Y=O,S) from the (A)over-tilda(2)A(1) state. Chemical Physics Letters. 1996;263:54-62. |
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Cui Q, Morokuma K, Stanton JF. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state. Non-adiabatic effects and S-T interaction. Chemical Physics Letters. 1996;263:46-53. |
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Cui Q, Musaev DG, Svensson M, Morokuma K. Analytical second derivatives for effective core potential. Application to transition structures of Cp(2)Ru(2)(mu-H)(4) and to the mechanism of reaction Cu+Ch(2)N(2). Journal of Physical Chemistry. 1996;100:10936-10944. |
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Huang H, Alvarez K, Cui Q, Barnhart TM, Snyder P, PennerHahn JE. Infrared spectroscopic characterization of cyanocuprates (vol 118, pg 8808, 1996). Journal of the American Chemical Society. 1996;118:12252-12252. |
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Liu RF, Cui Q, Dunn KM, Morokuma K. Ab initio molecular orbital study of the mechanism of photodissociation of trans-azomethane. Journal of Chemical Physics. 1996;105:2333-2345. |
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Cui Q, Musaev DG, Svensson M, Sieber S, Morokuma K. N-2 CLEAVAGE BY 3-COORDINATE GROUP-6 COMPLEXES - W(III) COMPLEXES WOULD-BE BETTER THAN MO(III) COMPLEXES. Journal of the American Chemical Society. 1995;117:12366-12367. |
