Qiang Cui

发表

Viewpoint on ACS PHYS Division Sponsored Virtual Seminars.

Ryan C. Fortenberry, Anne B. McCoy, Christy F. Landes, 2021, Journal of Physical Chemistry B.

Protein functional dynamics : from femtoseconds to milliseconds Preface

Markus Meuwly, Qiang Cui, Q. Cui, 2012 .

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2002, Structure.

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

Yang Yang, Haibo Yu, Qiang Cui, 2008, Journal of molecular biology.

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

Michael Gaus, Marcus Elstner, Qiang Cui, 2014, Journal of chemical theory and computation.

Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models

Arun Yethiraj, Zhe Wu, Qiang Cui, 2011 .

A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.

Jejoong Yoo, Qiang Cui, Q. Cui, 2013, Biophysical journal.

Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations

Qiang Cui, Xiaodong Zhang, Guohui Li, 2003 .

Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations

Martin Karplus, Qiang Cui, M. Karplus, 2000 .

Conservation and variation of structural flexibility in protein families.

Adam W Van Wynsberghe, Qiang Cui, Q. Cui, 2010, Structure.

Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models

Stephan Irle, Hu-Jun Qian, Puja Goyal, 2014, The journal of physical chemistry. B.

Ab initio molecular-orbital study of the trichlorine radical, Cl3

Michael C. Heaven, Keiji Morokuma, Alexey L. Kaledin, 1998 .

Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli

Jejoong Yoo, Yuye Tang, Xi Chen, 2009, Shi yan li xue = Journal of experimental mechanics.

A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

Martin Karplus, Marcus Elstner, Qiang Cui, 2002 .

Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.

Qiang Cui, Guohui Li, Q. Cui, 2004, Biophysical journal.

Many-Body Effects and Electrostatics in Biomolecules

Markus Meuwly, Pengyu Ren, Qiang Cui, 2016 .

FTO-Mediated Formation of N6-Hydroxymethyladenosine and N6-Formyladenosine in Mammalian RNA

Chuan He, Marcelo A. Nobrega, Guifang Jia, 2013, Nature Communications.

Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

Michael Gaus, Marcus Elstner, Qiang Cui, 2014, The journal of physical chemistry. B.

Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations

Qiang Cui, Guohui Li, Q. Cui, 2004 .

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.

Qiang Cui, Q. Cui, D. Riccardi, 2005, The Journal of chemical physics.

Specific Substates of Ras To Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments.

Yang Li, Klaus Gerwert, Sara Stephan, 2018, The journal of physical chemistry letters.

Activation mechanism of a signaling protein at atomic resolution from advanced computations.

Liang Ma, Qiang Cui, Q. Cui, 2007, Journal of the American Chemical Society.

Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies.

Hua Guo, Dingguo Xu, Qiang Cui, 2007, Journal of the American Chemical Society.

Detailed structure of the H2PO4(-)-guanosine diphosphate intermediate in Ras-GAP decoded from FTIR experiments by biomolecular simulations.

Klaus Gerwert, Till Rudack, Qiang Cui, 2012, Journal of the American Chemical Society.

QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments

Wei Yang, Donghong Min, Qiang Cui, 2010 .

Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

Martin Karplus, Qiang Cui, M. Karplus, 2003 .

Interactions between phosphate and water in solution: a natural bond orbital based analysis in a QM/MM framework.

Yang Yang, Qiang Cui, Q. Cui, 2007, The journal of physical chemistry. B.

Why do arginine and lysine organize lipids differently? Insights from coarse-grained and atomistic simulations.

Arun Yethiraj, Zhe Wu, Qiang Cui, 2013, The journal of physical chemistry. B.

A new coarse-grained model for water: the importance of electrostatic interactions.

Arun Yethiraj, Zhe Wu, Qiang Cui, 2010, The journal of physical chemistry. B.

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2004, Journal of molecular biology.

Many local motions cooperate to produce the adenylate kinase conformational transition.

Michael D. Daily, George N Phillips, Qiang Cui, 2010, Journal of molecular biology.

Application of elastic network models to proteins in the crystalline state.

George N Phillips, Qiang Cui, G. Phillips, 2009, Biophysical journal.

The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state.

Yang Yang, Qiang Cui, Q. Cui, 2009, The journal of physical chemistry. A.

pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications.

Qiang Cui, Q. Cui, D. Riccardi, 2007, The journal of physical chemistry. A.

Structural insight into substrate preference for TET-mediated oxidation

Cheng Luo, Ze Li, Lulu Hu, 2015, Nature.

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

Michael Gaus, Marcus Elstner, Qiang Cui, 2011, Journal of chemical theory and computation.

D. Riccardi, Q. Cui, and G. N. Phillips Jr. 2009. Application of elastic network models to proteins in the crystalline state. Biophys. J. 96:464-475

Qiang Cui, D. Riccardi, G. N. Phillips, 2009 .

Density functional tight binding: application to organic and biological molecules

Michael Gaus, Marcus Elstner, Qiang Cui, 2014 .

Ab initio MO studies on the photodissociation of C2H2 from the S1 (1Au) state. Non-adiabatic effects and S-T interaction

John F. Stanton, Keiji Morokuma, Qiang Cui, 1996 .

A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method

Efthimios Kaxiras, Martin Karplus, Marcus Elstner, 2001 .

Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

Guanhua Hou, Qiang Cui, Q. Cui, 2013, Journal of the American Chemical Society.

An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces.

Toshifumi Mori, Qiang Cui, R. Hamers, 2013, Journal of chemical theory and computation.

Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis.

Qiang Cui, Xiaodong Zhang, Q. Cui, 2002, Journal of the American Chemical Society.

Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water.

Puja Goyal, Marcus Elstner, Qiang Cui, 2011, The journal of physical chemistry. B.

Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine

Qiang Cui, Q. Cui, 2002 .

Importance of van der Waals Interactions in QM/MM Simulations.

Qiang Cui, Guohui Li, Q. Cui, 2004, The journal of physical chemistry. B.

N2 CLEAVAGE BY THREE-COORDINATE GROUP 6 COMPLEXES. W(III) COMPLEXES WOULD BE BETTER THAN MO(III) COMPLEXES

Djamaladdin G. Musaev, Keiji Morokuma, Mats Svensson, 1995 .

Analytical Second Derivatives for Effective Core Potential. Application to Transition Structures of Cp2Ru2(μ-H)4 and to the Mechanism of Reaction Cu + CH2N2

Djamaladdin G. Musaev, Keiji Morokuma, Qiang Cui, 1996 .

Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.

George N Phillips, Qiang Cui, G. Phillips, 2010, Biophysical journal.

Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies.

Hua Guo, Dingguo Xu, Qiang Cui, 2007, The journal of physical chemistry. A.

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.

Thomas Frauenheim, Xavier Prat-Resina, Marcus Elstner, 2006, Journal of the American Chemical Society.

Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models.

Arun Yethiraj, Qiang Cui, Q. Cui, 2014, Journal of chemical theory and computation.

Ab initio MO studies on the photodissociation of C2H2 from the S1(1Au) state. II. Mechanism involving triplet states

Keiji Morokuma, Qiang Cui, K. Morokuma, 1997 .

Sequence-dependent interaction of β-peptides with membranes.

Arun Yethiraj, Jagannath Mondal, Qiang Cui, 2010, The journal of physical chemistry. B.

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

Qiang Cui, Q. Cui, N. Ghosh, 2008, The journal of physical chemistry. B.

Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor.

Hua Guo, Qiang Cui, Q. Cui, 2008, Biochemistry.

QM/MM free energy simulations: recent progress and challenges

Yuko Okamoto, Shingo Ito, Victor Ovchinnikov, 2016, Molecular simulation.

Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase.

Martin Karplus, Qiang Cui, M. Karplus, 2003, Advances in protein chemistry.

Comparison of mode analyses at different resolutions applied to nucleic acid systems.

Adam W Van Wynsberghe, Qiang Cui, Q. Cui, 2005, Biophysical journal.

An implicit solvent model for SCC-DFTB with Charge-Dependent Radii.

Guanhua Hou, Qiang Cui, Q. Cui, 2010, Journal of chemical theory and computation.