QM/MM‐Methoden für biomolekulare Systeme
暂无分享,去创建一个
[1] Cristiano Ruch Werneck Guimarães,et al. Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase. , 2003, Journal of the American Chemical Society.
[2] J. Gascón,et al. QM/MM Study of the NMR Spectroscopy of the Retinyl Chromophore in Visual Rhodopsin. , 2005, Journal of chemical theory and computation.
[3] Walter Thiel,et al. Latrunculin analogues with improved biological profiles by "diverted total synthesis": preparation, evaluation, and computational analysis. , 2007, Chemistry.
[4] A. Laio,et al. Equilibrium free energies from nonequilibrium metadynamics. , 2006, Physical Review Letters.
[5] A. Crespo,et al. Heme protein oxygen affinity regulation exerted by proximal effects. , 2006, Journal of the American Chemical Society.
[6] Hans-Joachim Werner,et al. Local perturbative triples correction (T) with linear cost scaling , 2000 .
[7] Sally A. Hindle,et al. Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase , 2001 .
[8] G. Crooks. Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems , 1998 .
[9] A. Rauk,et al. QM/MM study of electron addition on protein disulfide bonds , 2006 .
[10] Charles L. Brooks,et al. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations , 2004, J. Comput. Chem..
[11] A. Lledós,et al. Some critical issues in the application of quantum mechanics/molecular mechanics methods to the study of transition metal complexes. , 2003, Faraday discussions.
[12] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[13] D. Chandler,et al. Transition pathways in a many-body system: Application to hydrogen-bond breaking in water , 1998 .
[14] Adrian J Mulholland,et al. Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase. , 2004, Chemical communications.
[15] K. Yoshizawa,et al. QM/MM Study on the Catalytic Mechanism of Benzene Hydroxylation over Fe-ZSM-5 , 2006 .
[16] A. Laio,et al. A variational definition of electrostatic potential derived charges , 2004 .
[17] J. Andrew McCammon,et al. Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies , 2003 .
[18] Jean-Louis Rivail,et al. Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method , 1996 .
[19] M. Sutcliffe,et al. Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: oxidation of tryptamine by aromatic amine dehydrogenase. , 2007, The journal of physical chemistry. B.
[20] G. Monard,et al. Determination of Enzymatic Reaction Pathways Using QM/MM Methods , 2003 .
[21] Sason Shaik,et al. The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. , 2002, Journal of the American Chemical Society.
[22] Walter Thiel,et al. QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction. , 2006, Journal of chemical theory and computation.
[23] Walter Thiel,et al. Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase , 2001 .
[24] S. French,et al. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts , 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[26] Steven J. Stuart,et al. Dynamical fluctuating charge force fields: Application to liquid water , 1994 .
[27] B. Grigorenko,et al. Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases. , 2006, Journal of chemical theory and computation.
[28] K. Yoshizawa,et al. Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase. , 2007, Chemistry.
[29] Q. Cui,et al. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. , 2005, The journal of physical chemistry. B.
[30] Toyokazu Ishida. Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process. , 2006, Biochemistry.
[31] C. Jarzynski. Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.
[32] Adrian J Mulholland,et al. Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling , 2006, Science.
[33] Jean-Louis Rivail,et al. Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method , 2002, J. Comput. Chem..
[34] K. Morokuma,et al. Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study. , 2006, The journal of physical chemistry. B.
[35] A. Laio,et al. Assessing the accuracy of metadynamics. , 2005, The journal of physical chemistry. B.
[36] Arieh Warshel,et al. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..
[37] Qiang Cui,et al. Importance of van der Waals Interactions in QM/MM Simulations. , 2004, The journal of physical chemistry. B.
[38] Neil A Burton,et al. Structure and redox properties of the protein, rubredoxin, and its ligand and metal mutants studied by electronic structure calculation. , 2006, The journal of physical chemistry. A.
[39] Bernard R. Brooks,et al. ENZYME MECHANISMS WITH HYBRID QUANTUM AND MOLECULAR MECHANICAL POTENTIALS.I. THEORETICAL CONSIDERATIONS , 1996 .
[40] Thom Vreven,et al. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. , 2006, Journal of chemical theory and computation.
[41] Àngels González-Lafont,et al. On the ionization state of the substrate in the active site of glutamate racemase. A QM/MM study about the importance of being zwitterionic. , 2006, The journal of physical chemistry. A.
[42] M. Karplus,et al. Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach , 1985, Biopolymers.
[43] Wilfred F van Gunsteren,et al. Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen: The Effect of Explicitly Including Solvent Polarization. , 2007, Journal of chemical theory and computation.
[44] Orlando Acevedo,et al. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. , 2007, Journal of chemical theory and computation.
[45] David Chandler,et al. Finding transition pathways: throwing ropes over rough mountain passes, in the dark , 1998 .
[46] Sergio Martí,et al. Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems. , 2005, Journal of chemical theory and computation.
[47] Yingkai Zhang,et al. Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9. , 2007, The journal of physical chemistry. B.
[48] I. H. Hillier,et al. A quantum mechanical/molecular mechanical model of inhibition of the enzyme phospholipase A2 , 1991 .
[49] J. Briggs,et al. Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes. , 2007, Biophysical journal.
[50] M. Karplus,et al. How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations , 2004, Science.
[51] Joachim Sauer,et al. Combining quantum mechanics and interatomic potential functions in ab initio studies of extended systems , 2000 .
[52] T. C. Bruice. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. , 2006, Chemical reviews.
[53] Walter Thiel,et al. Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase. , 2008, The Journal of chemical physics.
[54] Keiji Morokuma,et al. Protein environment facilitates O2 binding in non-heme iron enzyme. An insight from ONIOM calculations on isopenicillin N synthase (IPNS). , 2007, The journal of physical chemistry. B.
[55] Klaus Schulten,et al. Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. , 2006, Journal of the American Chemical Society.
[56] C. Dellago,et al. Autoionization in Liquid Water , 2001, Science.
[57] Guang-Fu Yang,et al. Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations. , 2006, Biophysical journal.
[58] Olivier Coulaud,et al. Linear scaling algorithm for the coordinate transformation problem of molecular geometry optimization , 2000 .
[59] W. V. van Berkel,et al. Structure and mechanism of para‐hydroxybenzoate hydroxylase , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[60] Weitao Yang,et al. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface , 2000 .
[61] R. Naik,et al. Computational study of the absorption spectra of green fluorescent protein mutants. , 2007, Biopolymers.
[62] Andrew E. Torda,et al. The GROMOS biomolecular simulation program package , 1999 .
[63] K. Gerwert,et al. Role of the arginine finger in Ras·RasGAP revealed by QM/MM calculations , 2007, FEBS letters.
[64] Christine M. Bathelt,et al. QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase. , 2005, Dalton transactions.
[65] M. Tuckerman,et al. Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein. , 2006, Journal of the American Chemical Society.
[66] Substrate binding in the active site of cytochrome P450cam , 2005 .
[67] J. VandeVondele,et al. Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces , 2002 .
[68] Xiaodong Zhang,et al. The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[69] W. L. Jorgensen,et al. Why urea eliminates ammonia rather than hydrolyzes in aqueous solution. , 2007, The journal of physical chemistry. B.
[70] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[71] A. Fornili,et al. Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding , 2003 .
[72] L. Pedersen,et al. Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics , 2006 .
[73] A. Mulholland,et al. CORRELATION OF CALCULATED ACTIVATION ENERGIES WITH EXPERIMENTAL RATE CONSTANTS FOR AN ENZYME CATALYZED AROMATIC HYDROXYLATION , 1998 .
[74] P. Callis,et al. Ab initio prediction of tryptophan fluorescence quenching by protein electric field enabled electron transfer. , 2007, The journal of physical chemistry. B.
[75] Y. Mo,et al. Deprotonation mechanism of NH4+ in the Escherichia coli ammonium transporter AmtB: insight from QM and QM/MM calculations. , 2007, Angewandte Chemie.
[76] Victor Guallar,et al. Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. , 2006, Journal of the American Chemical Society.
[77] Walter Thiel,et al. Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes. , 2005, The journal of physical chemistry. B.
[78] Jiali Gao,et al. Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry , 1996 .
[79] Martin Schütz,et al. Low-order scaling local electron correlation methods. V. Connected triples beyond (T): Linear scaling local CCSDT-1b , 2002 .
[80] Alexander D. MacKerell,et al. All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution , 2000 .
[81] K. Bravaya,et al. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. , 2007, Journal of the American Chemical Society.
[82] A. Mulholland,et al. Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity. , 2003, Current topics in medicinal chemistry.
[83] Kazuo Kitaura,et al. All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction. , 2006, The journal of physical chemistry. B.
[84] A. Warshel. Computer simulations of enzyme catalysis: methods, progress, and insights. , 2003, Annual review of biophysics and biomolecular structure.
[85] M. Freindorf,et al. Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin. , 2008, Journal of inorganic biochemistry.
[86] M. Swart. AddRemove: A new link model for use in QM/MM studies , 2003 .
[87] I. Komáromi,et al. Application of the IMOMM (Integrated Molecular Orbital Molecular Mechanics) Method for Biopolymers , 2002 .
[88] M. Alfonso-Prieto,et al. Versatility of the electronic structure of compound I in catalase-peroxidases. , 2007, Journal of the American Chemical Society.
[89] A. Mulholland,et al. Quantum chemical analysis of reaction paths in chorismate mutase: Conformational effects and electrostatic stabilization , 2007 .
[90] Computer modelling of enzyme reactions , 2003 .
[91] W. Berkel,et al. Biocatalytic Potential of p-Hydroxybenzoate Hydroxylase from Rhodococcus rhodnii 135 and Rhodococcus opacus 557 , 2004 .
[92] W. Richards,et al. Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction , 1995 .
[93] Richard A. Friesner,et al. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large‐scale modeling of chemistry in protein environments , 2000, J. Comput. Chem..
[94] H. Bernhard Schlegel,et al. Geometry optimization methods for modeling large molecules , 2003 .
[95] R. Friesner,et al. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. , 2005, Annual review of physical chemistry.
[96] Alexander D. MacKerell,et al. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. , 2005, Journal of chemical theory and computation.
[97] R. Friesner,et al. Frozen orbital QM/MM methods for density functional theory , 2000 .
[98] L. Cavallo,et al. Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations , 1998 .
[99] Peter Pulay,et al. An efficient direct method for geometry optimization of large molecules in internal coordinates , 1998 .
[100] Jiali Gao,et al. Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method , 2004 .
[101] Walter Thiel,et al. Enzymatic reactions of triosephosphate isomerase: A theoretical calibration study , 2002 .
[102] Yihan Shao,et al. YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model. , 2007, The journal of physical chemistry. A.
[103] A. Mulholland,et al. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex. , 2007, Journal of molecular graphics & modelling.
[104] Kazunari Yoshizawa,et al. Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): a DFT and QM/MM study. , 2006, Journal of the American Chemical Society.
[105] Yingkai Zhang,et al. Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures. , 2006, Journal of the American Chemical Society.
[106] Hao-Bo Guo,et al. Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity , 2007, Proceedings of the National Academy of Sciences.
[107] Donald G Truhlar,et al. Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. , 2006, Journal of the American Chemical Society.
[108] Walter Thiel,et al. Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration". , 2005, The Journal of chemical physics.
[109] Arieh Warshel,et al. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. , 2006, Chemical reviews.
[110] K. Mahnam,et al. A theoretical elucidation of bilirubin interaction with HSA's lysines: first electrostatic binding site in IIA subdomain. , 2007, Biophysical chemistry.
[111] Jiali Gao,et al. A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase. , 2006, Journal of the American Chemical Society.
[112] R. Wierenga,et al. The planar conformation of a strained proline ring: A QM/MM study , 2006, Proteins.
[113] Car,et al. Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.
[114] R A Friesner,et al. Quantum mechanical calculations on biological systems. , 1998, Current opinion in structural biology.
[115] V. Batista,et al. Computational studies of the primary phototransduction event in visual rhodopsin. , 2006, Accounts of chemical research.
[116] W. L. Jorgensen,et al. Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology. , 2007, Journal of chemical theory and computation.
[117] Adrian J Mulholland,et al. Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions , 2007, Chemistry Central journal.
[118] Sason Shaik,et al. Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism. , 2004, Journal of the American Chemical Society.
[119] Darrin M York,et al. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations. , 2005, Journal of chemical theory and computation.
[120] M. Field,et al. A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations , 1998 .
[121] Alexander D. MacKerell. Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..
[122] T. C. Bruice,et al. Comparison of formation of reactive conformers (NACs) for the Claisen rearrangement of chorismate to prephenate in water and in the E. coli mutase: the efficiency of the enzyme catalysis. , 2003, Journal of the American Chemical Society.
[123] U. Wahlgren,et al. Quantum chemical calculations of reduction potentials of AnO2(2+)/AnO2+ (An = U, Np, Pu, Am) and Fe3+/Fe2+ couples. , 2006, The journal of physical chemistry. A.
[124] U. Ryde,et al. NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S , 2005, Journal of biomolecular NMR.
[125] Kristina Nilsson,et al. Quantum refinement - a combination of quantum chemistry and protein crystallography. , 2003 .
[126] B. Grigorenko,et al. trans and cis Chromophore structures in the kindling fluorescent protein asFP595 , 2006 .
[127] Honggao Yan,et al. A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase. , 2006, The journal of physical chemistry. B.
[128] Brent A. Gregersen,et al. A charge‐scaling implementation of the variational electrostatic projection method , 2006, J. Comput. Chem..
[129] Donald G Truhlar,et al. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. , 2005, The journal of physical chemistry. A.
[130] Hua Guo,et al. Inhibitor binding by metallo-beta-lactamase IMP-1 from Pseudomonas aeruginosa: quantum mechanical/molecular mechanical simulations. , 2007, The journal of physical chemistry. B.
[131] Jiali Gao,et al. The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations. , 2007, Biochemistry.
[132] Ilme Schlichting,et al. Structure and chemistry of cytochrome P450. , 2005, Chemical reviews.
[133] W. Im,et al. Generalized solvent boundary potential for computer simulations , 2001 .
[134] Alessandra Magistrato,et al. Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations. , 2006, Organic & biomolecular chemistry.
[135] J. Mccammon,et al. Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. , 2007, Journal of the American Chemical Society.
[136] I. Tuñón,et al. QM/MM calculations of kinetic isotope effects in the chorismate mutase active site. , 2003, Organic & biomolecular chemistry.
[137] Ulf Ryde,et al. Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods , 2006 .
[138] A. Nemukhin,et al. Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure. , 2007, The journal of physical chemistry. B.
[139] Peter Margl,et al. A Combined Car−Parrinello QM/MM Implementation for ab Initio Molecular Dynamics Simulations of Extended Systems: Application to Transition Metal Catalysis , 1997 .
[140] Donald G. Truhlar,et al. Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method , 2004 .
[141] G. Colombo,et al. Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity , 2006 .
[142] M. Thompson,et al. QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone , 1996 .
[143] C. Suresh,et al. Role of Mg2+ and Ca2+ in DNA bending: evidence from an ONIOM-based QM-MM study of a DNA fragment. , 2006, The journal of physical chemistry. A.
[144] Pedro Alexandrino Fernandes,et al. Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere , 2007, J. Comput. Chem..
[145] P. Carloni,et al. Structure and function of vanadium haloperoxidases. , 2006, The journal of physical chemistry. B.
[146] Christoph Dellago,et al. On the calculation of reaction rate constants in the transition path ensemble , 1999 .
[147] György G. Ferenczy,et al. Quantum mechanical computations on very large molecular systems: The local self‐consistent field method , 1994, J. Comput. Chem..
[148] H. Bernhard Schlegel,et al. Methods for optimizing large molecules. Part III. An improved algorithm for geometry optimization using direct inversion in the iterative subspace (GDIIS) , 2002 .
[149] Milan Hodošček,et al. A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region , 1999 .
[150] P. Ordejón,et al. A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase , 2003 .
[151] Hua Guo,et al. Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study. , 2006, Biochemistry.
[152] Yan Zhang,et al. Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems. , 2008, Journal of chemical theory and computation.
[153] Sergio Martí,et al. Theoretical insights in enzyme catalysis. , 2004, Chemical Society reviews.
[154] C. Dellago,et al. Transition Path Sampling , 2005 .
[155] M. Alfonso-Prieto,et al. A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures , 2006 .
[156] B. Grigorenko,et al. Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments , 2002 .
[157] Cristiano Ruch Werneck Guimarães,et al. Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate. , 2005, Journal of chemical theory and computation.
[158] D. Truhlar,et al. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. , 2007, Journal of chemical theory and computation.
[159] A. Mulholland,et al. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase. , 1999, Journal of molecular graphics & modelling.
[160] Bernard R. Brooks,et al. Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations , 2007, J. Comput. Chem..
[161] V. Batista,et al. QM/MM Models of the O2-Evolving Complex of Photosystem II. , 2006, Journal of chemical theory and computation.
[162] Àngels González-Lafont,et al. Geometry optimization and transition state search in enzymes: Different options in the microiterative method , 2004 .
[163] Mark S. Gordon,et al. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry , 2001 .
[164] K. Yoshizawa,et al. Water-assisted oxo mechanism for heme metabolism. , 2005, Journal of the American Chemical Society.
[165] K. Morokuma,et al. ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition , 1996 .
[166] Nathalie Reuter,et al. Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches , 2000 .
[167] Ursula Rothlisberger,et al. The protonation state of the Glu-71/Asp-80 residues in the KcsA potassium channel: a first-principles QM/MM molecular dynamics study. , 2007, Biophysical journal.
[168] Wei Yang,et al. Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials. , 2004, The Journal of chemical physics.
[169] David P. Landau,et al. Determining the density of states for classical statistical models by a flat-histogram random walk☆ , 2002 .
[170] M. Tuckerman,et al. On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles , 2002 .
[171] Yingkai Zhang,et al. Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. , 2007, The Journal of chemical physics.
[172] Jiali Gao,et al. Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials , 1992 .
[173] Xiaodong Zhang,et al. A definitive mechanism for chorismate mutase. , 2005, Biochemistry.
[174] Victor Guallar,et al. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. , 2004, Journal of the American Chemical Society.
[175] Victor Guallar,et al. The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study. , 2006, Journal of the American Chemical Society.
[176] Weitao Yang,et al. Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase. , 2006, The journal of physical chemistry. A.
[177] Thomas Frauenheim,et al. An approximate DFT method for QM/MM simulations of biological structures and processes , 2003 .
[178] Jans H Alzate-Morales,et al. A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity. , 2007, Biophysical journal.
[179] S. Piana,et al. Hybrid Car-Parrinello/molecular mechanics modelling of transition metal complexes: Structure, dynamics and reactivity , 2002 .
[180] A. Warshel,et al. Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution , 1998 .
[181] H. Bernhard Schlegel,et al. Methods for geometry optimization of large molecules. I. An O(N2) algorithm for solving systems of linear equations for the transformation of coordinates and forces , 1998 .
[182] D. Truhlar,et al. Mechanisms and free energies of enzymatic reactions. , 2006, Chemical reviews.
[183] M. Civera,et al. Extremely localized molecular orbitals: theory and applications , 2007 .
[184] I. Tuñón,et al. Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes. , 2006, The journal of physical chemistry. B.
[185] U. Rothlisberger,et al. Enantioselective Palladium-Catalyzed Hydrosilylation of Styrene: Influence of Electronic and Steric Effects on Enantioselectivity and Catalyst Design via Hybrid QM/MM Molecular Dynamics Simulations , 2006 .
[186] Sergio Martí,et al. A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization? , 2004, Journal of the American Chemical Society.
[187] Frederick R. Manby,et al. Linear scaling local coupled cluster theory with density fitting. Part I: 4-external integrals , 2003 .
[188] Paul Tavan,et al. A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields , 1999 .
[189] Weitao Yang,et al. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. , 2004, The Journal of chemical physics.
[190] Frank Neese,et al. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study , 2006, J. Comput. Chem..
[191] V. Moliner,et al. A quantum mechanics/molecular mechanics study of the catalytic mechanism of the thymidylate synthase. , 2007, Biochemistry.
[192] Adrian J Mulholland,et al. Modelling enzyme reaction mechanisms, specificity and catalysis. , 2005, Drug discovery today.
[193] Stanley K. Burt,et al. Flexible effective fragment QM/MM method: Validation through the challenging tests , 2003, J. Comput. Chem..
[194] Iris Antes,et al. On the Treatment of Link Atoms in Hybrid Methods , 1998 .
[195] I. H. Hillier,et al. CHEMICAL REACTIVITY STUDIED BY HYBRID QM/MM METHODS , 1999 .
[196] Alessandro Laio,et al. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. , 2003, Physical review letters.
[197] Alexander D. MacKerell,et al. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model , 2004, J. Comput. Chem..
[198] Arieh Warshel,et al. Energetics and Dynamics of Enzymatic Reactions , 2001 .
[199] J. Bertrán,et al. Conformational equilibrium of chorismate. A QM/MM theoretical study combining statistical simulations and geometry optimisations in gas phase and in aqueous solution , 2003 .
[200] S. Senapati,et al. In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions. , 2006, Journal of medicinal chemistry.
[201] Harry A. Stern,et al. Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Initio Quantum Chemistry , 1999 .
[202] Pengyu Y. Ren,et al. Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations , 2002, J. Comput. Chem..
[203] Gino A DiLabio,et al. Efficient silicon surface and cluster modeling using quantum capping potentials. , 2005, The Journal of chemical physics.
[204] Haibo Yu,et al. Accounting for polarization in molecular simulation , 2005, Comput. Phys. Commun..
[205] Richard A. Friesner,et al. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide , 1999 .
[206] Iwao Ohmine,et al. Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method , 2000 .
[207] Alexander D. MacKerell,et al. Polarizable empirical force field for alkanes based on the classical Drude oscillator model. , 2005, The journal of physical chemistry. B.
[208] Teodoro Laino,et al. QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis. , 2007, The journal of physical chemistry. B.
[209] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[210] Ulf Ryde,et al. Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements. , 2007, Journal of the American Chemical Society.
[211] James A Platts,et al. A QM/MM study of cisplatin-DNA oligonucleotides: from simple models to realistic systems. , 2006, Chemistry.
[212] Marat Valiev,et al. Combined quantum mechanical and molecular mechanics studies of the electron-transfer reactions involving carbon tetrachloride in solution. , 2008, The journal of physical chemistry. A.
[213] K. Merz,et al. Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems , 1999 .
[214] R. Friesner,et al. Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. , 2007, Journal of the American Chemical Society.
[215] F. Neese,et al. Multireference ab initio quantum mechanics/molecular mechanics study on intermediates in the catalytic cycle of cytochrome P450(cam). , 2008, The journal of physical chemistry. A.
[216] Dongqi Wang,et al. 51V NMR chemical shifts calculated from QM/MM models of vanadium chloroperoxidase. , 2007, Chemistry.
[217] Donald G Truhlar,et al. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. , 2007, The journal of physical chemistry. B.
[218] W. Goddard,et al. Exploring the molecular mechanism for color distinction in humans. , 2006, The journal of physical chemistry. B.
[219] H. Senn,et al. QM/MM Methods for Biological Systems , 2006 .
[220] Linus Pauling,et al. Molecular Architecture and Biological Reactions , 1946 .
[221] S. Shaik,et al. What is the active species of cytochrome P450 during camphor hydroxylation? QM/MM studies of different electronic states of compound I and of reduced and oxidized iron-oxo intermediates. , 2007, Journal of the American Chemical Society.
[222] Ian H. Williams,et al. Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase , 1999 .
[223] A. Roitberg,et al. Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase. , 2005, Journal of the American Chemical Society.
[224] Thom Vreven,et al. Geometry optimization with QM/MM methods II: Explicit quadratic coupling , 2006 .
[225] Nathaniel O. J. Malcolm,et al. Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent , 1998 .
[226] Alessandro Laio,et al. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations , 2002 .
[227] Toru Nakayama,et al. Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase. , 2006, Biochemistry.
[228] W. L. Jorgensen,et al. Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. , 2006, Journal of the American Chemical Society.
[229] N. Burton,et al. Mechanism of nitrite reduction at T2Cu centers: electronic structure calculations of catalysis by copper nitrite reductase and by synthetic model compounds. , 2007, The journal of physical chemistry. B.
[230] Stefan Fischer,et al. Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. , 2006, Biochemistry.
[231] K. Schulten,et al. PcrA helicase, a prototype ATP-driven molecular motor. , 2006, Structure.
[232] Marc Albe,et al. The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials , 2000 .
[233] P. Carloni,et al. Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study. , 2006, The journal of physical chemistry. B.
[234] Sason Shaik,et al. Two states and two more in the mechanisms of hydroxylation and epoxidation by cytochrome P450. , 2005, Journal of the American Chemical Society.
[235] J. Rivail,et al. The Local Self-Consistent Field Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems , 1998 .
[236] Bernard R. Brooks,et al. Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase , 2003 .
[237] C. Jarzynski,et al. A “fast growth” method of computing free energy differences , 2001 .
[238] José M. Lluch,et al. The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface , 2002 .
[239] P. Sherwood,et al. Identification and Characterization of Active Sites and Their Catalytic Processes—the Cu/ZnO Methanol Catalyst , 2003 .
[240] M. Karplus,et al. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. , 2003, Angewandte Chemie.
[241] Efthimios Kaxiras,et al. A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method , 2001 .
[242] D. Truhlar,et al. Quantum mechanical methods for enzyme kinetics. , 2003, Annual review of physical chemistry.
[243] Gerrit Groenhof,et al. Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein. , 2004, Journal of the American Chemical Society.
[244] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[245] F. Kleinhans. Show Me the Dog , 2006, Science.
[246] Kenneth M. Merz,et al. Calculation of solvation free energies using a density functional/molecular dynamics coupled potential , 1993 .
[247] M. Parrinello,et al. Solvent effects on charge spatial extent in DNA and implications for transfer. , 2007, Physical review letters.
[248] Kenneth M Merz,et al. Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement. , 2006, Journal of chemical theory and computation.
[249] B. Hoffman,et al. Rapid freeze-quench ENDOR study of chloroperoxidase compound I: the site of the radical. , 2006, Journal of the American Chemical Society.
[250] Arieh Warshel,et al. Ab Initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution , 2002 .
[251] Arieh Warshel,et al. Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin , 1998 .
[252] Walter Thiel,et al. QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. , 2008, Physical chemistry chemical physics : PCCP.
[253] Sason Shaik,et al. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. , 2005, Chemical reviews.
[254] P. Kollman,et al. Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis? , 2002 .
[255] Bernard R Brooks,et al. Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms. , 2007, The journal of physical chemistry. A.
[256] Marat Valiev,et al. Hybrid approach for free energy calculations with high-level methods: application to the SN2 reaction of CHCl3 and OH- in water. , 2007, The Journal of chemical physics.
[257] M. Karplus,et al. Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .
[258] U. Rothlisberger,et al. Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods , 2006 .
[259] Steven J. Stuart,et al. Potentials and Algorithms for Incorporating Polarizability in Computer Simulations , 2003 .
[260] Lars Ridder,et al. Ab initio QM/MM modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase , 2003 .
[261] Olivier Coulaud,et al. An efficient method for the coordinate transformation problem of massively three-dimensional networks , 2001 .
[262] Adrian J Mulholland,et al. Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization. , 2005, Chemical communications.
[263] U. Ryde,et al. Theoretical study of structure of catalytic copper site in nitrite reductase , 2005 .
[264] Alessandro Laio,et al. D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations , 2002 .
[265] D. Zahn. Unprejudiced identification of reaction mechanisms from biased transition path sampling. , 2005, The Journal of chemical physics.
[266] Self-Consistent Strictly Localized Orbitals. , 2007, Journal of chemical theory and computation.
[267] Martin J. Field,et al. Simulating enzyme reactions: Challenges and perspectives , 2002, J. Comput. Chem..
[268] Richard J. Hall,et al. Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase , 2000 .
[269] Sason Shaik,et al. QM/MM study of mechanisms for compound I formation in the catalytic cycle of cytochrome P450cam. , 2006, Journal of the American Chemical Society.
[270] R. Car,et al. Mapping potential energy surfaces. , 2004, The Journal of chemical physics.
[271] Raquel Castillo,et al. Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis. , 2006, Biochemistry.
[272] V. Batista,et al. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. , 2007, Current opinion in structural biology.
[273] A. Warshel,et al. Calculations of electrostatic interactions in biological systems and in solutions , 1984, Quarterly Reviews of Biophysics.
[274] Mark S. Gordon,et al. An effective fragment method for modeling solvent effects in quantum mechanical calculations , 1996 .
[275] Arieh Warshel,et al. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .
[276] M Karplus,et al. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. , 1989, Journal of molecular biology.
[277] Jingjing Zheng,et al. Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies , 2007, J. Comput. Chem..
[278] Ursula Rothlisberger,et al. Polarization effects and charge transfer in the KcsA potassium channel. , 2006, Biophysical chemistry.
[279] Patrik Rydberg,et al. Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase. , 2006, The Journal of chemical physics.
[280] J. Vervoort,et al. Modelling flavin and substrate substituent effects on the activation barrier and rate of oxygen transfer by p‐hydroxybenzoate hydroxylase , 2000, FEBS letters.
[281] Walter Thiel,et al. QM/MM studies of enzymes. , 2007, Current opinion in chemical biology.
[282] Xiche Hu,et al. Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis. , 2006, The journal of physical chemistry. A.
[283] Lars Ridder,et al. Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase. , 2007, Biochemistry.
[284] Alexander D. MacKerell. Chapter 7 Empirical Force Fields for Proteins: Current Status and Future Directions , 2005 .
[285] S. Hasnain,et al. Active site structures and the redox properties of blue copper proteins: atomic resolution structure of azurin II and electronic structure calculations of azurin, plastocyanin and stellacyanin. , 2006, Dalton transactions.
[286] Grubmüller,et al. Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[287] Duocarmycins binding to DNA investigated by molecular simulation. , 2006, The journal of physical chemistry. B.
[288] P. Kollman,et al. Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide , 1995 .
[289] Hao Hu,et al. Dual-topology/dual-coordinate free-energy simulation using QM/MM force field. , 2005, The Journal of chemical physics.
[290] Frank Neese,et al. Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters. , 2005, Journal of the American Chemical Society.
[291] Tiqing Liu,et al. Short range photoinduced electron transfer in proteins : QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins , 2006 .
[292] C. Dellago,et al. Equilibrium free energies from fast-switching trajectories with large time steps. , 2005, The Journal of chemical physics.
[293] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[294] Qiang Cui,et al. Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations , 2003 .
[295] Q. Cui,et al. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. , 2005, The journal of physical chemistry. B.
[296] Yingkai Zhang,et al. Pseudobond ab initio QM/MM approach and its applications to enzyme reactions , 2006 .
[297] U. Ryde,et al. Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases. , 2006, Journal of inorganic biochemistry.
[298] Kristina Nilsson,et al. Protonation status of metal-bound ligands can be determined by quantum refinement. , 2004, Journal of inorganic biochemistry.
[299] H. Grubmüller,et al. Predicting unimolecular chemical reactions: Chemical flooding , 2002 .
[300] Tai-Sung Lee,et al. A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .
[301] Yuji Sugita,et al. New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals , 2007 .
[302] Hao Hu,et al. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. , 2008, Annual review of physical chemistry.
[303] S. Shaik,et al. The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: a QM/MM study. , 2006, The journal of physical chemistry. B.
[304] X. Biarnés,et al. Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations. , 2006, The Journal of biological chemistry.
[305] D. Gao,et al. Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase , 2005, Proteins.
[306] Hua Guo,et al. Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies. , 2007, Journal of the American Chemical Society.
[307] K. Morokuma,et al. Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method , 2003 .
[308] Alexander D. MacKerell,et al. All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .
[309] Sergio Martí,et al. A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase. , 2007, Chemistry.
[310] A QM/MM approach with effective fragment potentials applied to the dipeptide–water structures , 2002 .
[311] Maurizio Sironi,et al. On the suitability of strictly localized orbitals for hybrid QM/MM calculations , 2006, J. Comput. Chem..
[312] P. Kollman,et al. Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution , 1998 .
[313] M. W. van der Kamp,et al. Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl‐CoA enolization in citrate synthase , 2007, Proteins.
[314] A. Cavalli,et al. Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. , 2007, Chemistry.
[315] L. Cavallo,et al. Towards more realistic computational modeling of homogenous catalysis by density functional theory: combined QM/MM and ab initio molecular dynamics , 1999 .
[316] Victor Guallar,et al. Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450 , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[317] V. Buss,et al. Origin and consequences of steric strain in the rhodopsin binding pocket. , 2006, Biochemistry.
[318] Walter Thiel,et al. Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians. , 2008, Journal of chemical theory and computation.
[319] Sergio Martí,et al. Hybrid QM/MM Potentials of Mean Force with Interpolated Corrections , 2004 .
[320] C. Kölmel,et al. Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs , 1997 .
[321] M. Sutcliffe,et al. Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.
[322] J. Gao,et al. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.
[323] John E. Adams,et al. Reaction path Hamiltonian for polyatomic molecules , 1980 .
[324] Xiaodong Zhang,et al. Histone lysine methyltransferase SET7/9: formation of a water channel precedes each methyl transfer. , 2007, Biochemistry.
[325] Weitao Yang,et al. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations. , 2004, The Journal of chemical physics.
[326] J. Giraldo,et al. The catalytic power of enzymes: Conformational selection or transition state stabilization? , 2006, FEBS letters.
[327] Thomas S. Hofer,et al. Coordination and ligand exchange dynamics of solvated metal ions , 2005 .
[328] Guillaume Lamoureux,et al. Peptide Hydrolysis in Thermolysin: Ab Initio QM/MM Investigation of the Glu143-Assisted Water Addition Mechanism. , 2007, Journal of chemical theory and computation.
[329] M. Meuwly. On the influence of the local environment on the CO stretching frequencies in native myoglobin: assignment of the B-states in MbCO. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.
[330] V. Vasilyev,et al. Tetrahedral intermediate formation in the acylation step of acetylcholinesterases. A combined quantum chemical and molecular mechanical model , 1994 .
[331] Jiali Gao,et al. Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model , 1997, J. Comput. Chem..
[332] Christoph Dellago,et al. Sampling ensembles of deterministic transition pathways , 1998 .
[333] P. Blöchl,et al. Towards solvation simulations with a combined ab initio molecular dynamics and molecular mechanics approach , 2000 .
[334] Marat Valiev,et al. Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment. , 2006, The Journal of chemical physics.
[335] Hua Guo,et al. Catalytic Mechanism of Class B2 Metallo-β-lactamase* , 2006, Journal of Biological Chemistry.
[336] T. C. Bruice,et al. Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants). , 2003, Journal of the American Chemical Society.
[337] Weitao Yang,et al. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase. , 2007, Journal of chemical theory and computation.
[338] A. Mulholland. The QM/MM Approach to Enzymatic Reactions , 2001 .
[339] S. Shaik,et al. Two-state reactivity, electromerism, tautomerism, and "surprise" isomers in the formation of compound II of the enzyme horseradish peroxidase from the principal species, compound I. , 2006, Journal of the American Chemical Society.
[340] Walter Thiel,et al. Exploiting QM/MM Capabilities in Geometry Optimization: A Microiterative Approach Using Electrostatic Embedding. , 2007, Journal of chemical theory and computation.
[341] Li Xie,et al. Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes. , 2004, The Journal of chemical physics.
[342] Keiji Morokuma,et al. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n‐butane conformation and SN2 reaction: RCl+Cl− , 1996 .
[343] Harry A. Stern,et al. Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests , 2002, J. Comput. Chem..
[344] Ulf Ryde,et al. Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide. , 2007, Inorganic chemistry.
[345] G. Crooks. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[346] Wei Yang,et al. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations. , 2007, The Journal of chemical physics.
[347] Helmut Grubmüller,et al. Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. , 2007, Journal of the American Chemical Society.
[348] Frederick R. Manby,et al. Fast linear scaling second-order Møller-Plesset perturbation theory (MP2) using local and density fitting approximations , 2003 .
[349] Walter Thiel,et al. Looking at self-consistent-charge density functional tight binding from a semiempirical perspective. , 2007, The journal of physical chemistry. A.
[350] Margaret M. Hurley,et al. Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules , 2002 .
[351] M. Fraaije,et al. Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. , 2006, Journal of biotechnology.
[352] W. Lubitz,et al. Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study. , 2006, Physical chemistry chemical physics : PCCP.
[353] Adrian J Mulholland,et al. High-accuracy computation of reaction barriers in enzymes. , 2006, Angewandte Chemie.
[354] J. King,et al. Mechanism of the highly efficient quenching of tryptophan fluorescence in human gammaD-crystallin. , 2006, Biochemistry.
[355] S. Shaik,et al. Structural characterization of the fleeting ferric peroxo species in myoglobin: experiment and theory. , 2007, Journal of the American Chemical Society.
[356] David R. Klug,et al. Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations , 2007, J. Comput. Chem..
[357] David Chandler,et al. Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.
[358] Bohdan Waszkowycz,et al. A theoretical study of hydrolysis by phospholipase A2: the catalytic role of the active site and substrate specificity , 1990 .
[359] M. Martí,et al. Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases , 2007, Proteins.
[360] Martin J. Field,et al. Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential , 1987 .
[361] M. Karplus,et al. A charge-scaling method to treat solvent in QM/MM simulations , 2003 .
[362] Thomas Frauenheim,et al. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. , 2006, Journal of the American Chemical Society.
[363] Christopher J. R. Illingworth,et al. Classical polarization in hybrid QM/MM methods. , 2006, The journal of physical chemistry. A.
[364] B. Grigorenko,et al. Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras‐GAP proteins as rationalized by ab initio QM/MM simulations , 2006, Proteins.
[365] Sason Shaik,et al. Principal active species of horseradish peroxidase, compound I: a hybrid quantum mechanical/molecular mechanical study. , 2005, Journal of the American Chemical Society.
[366] D. Landau,et al. Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.
[367] Sándor Suhai,et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .
[368] S. Shaik,et al. The effect of a water molecule on the mechanism of formation of compound 0 in horseradish peroxidase. , 2007, Journal of the American Chemical Society.
[369] M. Klein,et al. Proton shuttles and phosphatase activity in soluble epoxide hydrolase. , 2007, Journal of the American Chemical Society.
[370] Àngels González-Lafont,et al. A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase‐1 , 2007, J. Comput. Chem..
[371] Ulf Ryde,et al. Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase. , 2005, Journal of chemical theory and computation.
[372] M. W. van der Kamp,et al. Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase. , 2007, Journal of molecular graphics & modelling.
[373] S. Schwartz,et al. How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study. , 2005, Journal of the American Chemical Society.
[374] Adrian J Mulholland,et al. Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling. , 2005, Journal of the American Chemical Society.
[375] Gregory K. Schenter,et al. Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization , 1995 .
[376] S. Shaik,et al. Compound I of nitric oxide synthase: the active site protonation state. , 2007, Journal of the American Chemical Society.
[377] M. Karplus,et al. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[378] Thom Vreven,et al. Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints , 2003, J. Comput. Chem..
[379] Paul Sherwood,et al. Zeolite structure and reactivity by combined quantum-chemical- classical calculations , 1999 .
[380] U. Ryde,et al. A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases. , 2007, Inorganic chemistry.
[381] J. Bertrán,et al. Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case. , 2003, Chemistry.
[382] D. Deerfield,et al. Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. , 2007, Biochemistry.
[383] T. C. Bruice,et al. The near attack conformation approach to the study of the chorismate to prephenate reaction , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[384] Jiali Gao,et al. Solvatochromic Shifts of the n → π* Transition of Acetone from Steam Vapor to Ambient Aqueous Solution: A Combined Configuration Interaction QM/MM Simulation Study Incorporating Solvent Polarization. , 2007, Journal of chemical theory and computation.
[385] Feliu Maseras,et al. IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..
[386] Donald G. Truhlar,et al. Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics , 2004 .
[387] I. Tuñón,et al. Enzymatic effects on reactant and transition states. The case of chalcone isomerase. , 2007, Journal of the American Chemical Society.
[388] Arieh Warshel,et al. On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. , 2005, The journal of physical chemistry. B.
[389] Iris Antes,et al. Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods , 1999 .
[390] Adrian J Mulholland,et al. Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. , 2004, Journal of the American Chemical Society.
[391] Martin Schütz,et al. Low-order scaling local electron correlation methods. III. Linear scaling local perturbative triples correction (T) , 2000 .
[392] A. Warshel,et al. Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. , 2003, Advances in protein chemistry.
[393] C. Jarzynski. Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach , 1997, cond-mat/9707325.
[394] K. Schulten,et al. Calculating potentials of mean force from steered molecular dynamics simulations. , 2004, The Journal of chemical physics.
[395] K. Yoshizawa,et al. Catalytic mechanism of dopamine β-monooxygenase mediated by Cu(III)-oxo , 2006 .
[396] Lars Ridder,et al. Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A β-lactamase , 2006 .
[397] W. L. Jorgensen,et al. Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. , 2006, The Journal of organic chemistry.
[398] M. Bühl,et al. Simulation of 59Co NMR chemical shifts in aqueous solution. , 2005, Chemistry.
[399] Jon Baker,et al. Geometry optimization in delocalized internal coordinates: An efficient quadratically scaling algorithm for large molecules , 1999 .
[400] Christoph Dellago,et al. Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements , 1998 .
[401] Ulf Ryde,et al. The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations , 1996, J. Comput. Aided Mol. Des..
[402] Sergio Martí,et al. Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems. [J. Chem. Theory Comput. 1, 1008-1016 (2005)]. , 2006, Journal of chemical theory and computation.
[403] Dongqi Wang,et al. Quantum and molecular mechanical study of the first proton transfer in the catalytic cycle of cytochrome P450cam and its mutant D251N. , 2008, The journal of physical chemistry. B.
[404] Guohui Li,et al. pKa calculations with QM/MM free energy perturbations , 2003 .
[405] Ivano Tavernelli,et al. Optical spectra of Cu(II)-azurin by hybrid TDDFT-molecular dynamics simulations. , 2007, The journal of physical chemistry. B.
[406] T. C. Bruice,et al. Enzymes do what is expected (chalcone isomerase versus chorismate mutase). , 2003, Journal of the American Chemical Society.
[407] D. Truhlar,et al. QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .
[408] K. Morokuma,et al. A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES , 1999 .
[409] Arieh Warshel,et al. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. , 2006, The journal of physical chemistry. B.
[410] William L Jorgensen,et al. Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations. , 2007, Journal of chemical theory and computation.
[411] U. Ryde,et al. The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement. , 2004, Biophysical journal.
[412] Lars Ridder,et al. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction. , 2004, Organic & biomolecular chemistry.
[413] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[414] G. McIntyre,et al. H-X bond activation via hydrogen transfer to hydride in ruthenium N-heterocyclic carbene complexes : Density functional and synthetic studies , 2006 .
[415] Brent A. Gregersen,et al. Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations. , 2005, The journal of physical chemistry. B.
[416] S. Shaik,et al. QM/MM Study of the Product−Enzyme Complex in P450cam Catalysis , 2004 .
[417] H. Schlegel,et al. A combined method for determining reaction paths, minima, and transition state geometries , 1997 .
[418] Weitao Yang,et al. Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods. , 2005, The Journal of chemical physics.
[419] Jan H. Jensen,et al. QM/MM Boundaries Across Covalent Bonds: A Frozen Localized Molecular Orbital-Based Approach for the Effective Fragment Potential Method , 2000 .
[420] Xiaodong Zhang,et al. A quantum mechanics/molecular mechanics study of the catalytic mechanism and product specificity of viral histone lysine methyltransferase. , 2007, Biochemistry.
[421] Jiali Gao,et al. Solvent effects on the nπ* transition of pyrimidine in aqueous solution , 1997 .
[422] Kenneth M. Merz,et al. Mechanism of the human carbonic anhydrase II-catalyzed hydration of carbon dioxide , 1992 .
[423] Walter Thiel,et al. The resting state of p450cam A QM/MM study , 2004 .
[424] M. Sierka,et al. Hybrid Quantum Mechanics/ Molecular Mechanics Methods and their Application , 2005 .
[425] S. Shaik,et al. In silico design of a mutant of cytochrome P450 containing selenocysteine. , 2006, Journal of the American Chemical Society.
[426] Jiali Gao,et al. Excited state intramolecular proton transfer in 1-(trifluoroacetylamino)naphthaquinone: a CASPT2//CASSCF computational study , 2006 .
[427] B. Grigorenko,et al. Modeling dioxygen binding to the non‐heme iron‐containing enzymes , 2006 .
[428] J. G. Snijders,et al. A discrete solvent reaction field model within density functional theory , 2003 .
[429] Walter Thiel,et al. Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase: A Case Study for QM/MM Molecular Dynamics. , 2005, Journal of chemical theory and computation.
[430] Todd J Martínez,et al. Multicentered valence electron effective potentials: a solution to the link atom problem for ground and excited electronic states. , 2006, The Journal of chemical physics.
[431] Jeremy N. Harvey,et al. QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase , 2006, J. Comput. Chem..
[432] Kristina Nilsson,et al. Quantum chemistry can locally improve protein crystal structures. , 2003, Journal of the American Chemical Society.
[433] Ruth Nussinov,et al. QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. , 2007, The journal of physical chemistry. B.
[434] U. Ryde,et al. Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. , 2006, The journal of physical chemistry. B.
[435] T. Schlick,et al. DNA Polymerase β Catalysis: Are Different Mechanisms Possible? , 2007 .
[436] F. Maseras. Hybrid Quantum Mechanics/Molecular Mechanics Methods in Transition Metal Chemistry , 1999 .
[437] Wilfred F. van Gunsteren,et al. Development of a simple, self-consistent polarizable model for liquid water , 2003 .
[438] William L Jorgensen,et al. Cope elimination: elucidation of solvent effects from QM/MM simulations. , 2006, Journal of the American Chemical Society.
[439] Jeremy C. Smith,et al. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin , 2006, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.
[440] Hiroshi Nakatsuji,et al. On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study , 2006 .
[441] T. Kerdcharoen,et al. Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach. , 2006, The journal of physical chemistry. A.
[442] M. Karplus,et al. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .
[443] Zexing Cao Prof.,et al. Deprotonation Mechanism of NH4+ in the Escherichia coli Ammonium Transporter AmtB: Insight from QM and QM/MM Calculations† , 2007 .
[444] Jodi Basner,et al. Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis. , 2006, Chemical reviews.
[445] Jon Baker,et al. Geometry optimization of large biomolecules in redundant internal coordinates , 2000 .
[446] Jean-Louis Rivail,et al. HYBRID CLASSICAL QUANTUM FORCE FIELD FOR MODELING VERY LARGE MOLECULES , 1996 .
[447] Hua Guo,et al. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies. , 2007, The journal of physical chemistry. A.
[448] S. Saito,et al. Proton transfer and associated molecular rearrangements in the photocycle of photoactive yellow protein: role of water molecular migration on the proton transfer reaction. , 2007, Journal of Physical Chemistry B.
[449] M. Vincent,et al. Computer simulation of zeolite structure and reactivity using embedded cluster methods , 1997 .
[450] J. Gready,et al. Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase. , 2007, Journal of chemical theory and computation.
[451] Andrew E. Torda,et al. Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..
[452] Hans-Joachim Werner,et al. Low-order scaling local electron correlation methods. IV. Linear scaling local coupled-cluster (LCCSD) , 2001 .
[453] Keiji Morokuma,et al. Application of the New “Integrated MO + MM” (IMOMM) Method to the Organometallic Reaction Pt(PR3)2 + H2 (R = H, Me, t-Bu, and Ph) , 1996 .
[454] I. Tuñón,et al. Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction. , 2006, Journal of Physical Chemistry B.
[455] A. Warshel,et al. Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[456] P. Kollman,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .
[457] Xuri Huang,et al. Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis: a hybrid QM/MM study. , 2006, Journal of structural biology.
[458] Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions , 2002 .
[459] Scott F. Smith,et al. Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution , 1985 .
[460] Bernard R. Brooks,et al. Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method , 2002 .
[461] Alexey A. Sokol,et al. QM/MM modelling of the TS-1 catalyst using HPCx , 2006 .
[462] Qiang Cui,et al. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. , 2005, The Journal of chemical physics.
[463] James Andrew McCammon,et al. Molecular Dynamics Simulations with Interaction Potentials Including Polarization Development of a Noniterative Method and Application to Water , 1990 .
[464] Ulf Ryde,et al. EXAFS structure refinement supplemented by computational chemistry , 2006 .
[465] F. Manby,et al. Explicitly correlated second-order perturbation theory using density fitting and local approximations. , 2006, The Journal of chemical physics.
[466] W. Thiel,et al. Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin. , 2007, Biophysical journal.
[467] Dongqi Wang,et al. New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0. , 2005, The journal of physical chemistry. B.
[468] Preston Moore,et al. Metadynamics as a tool for exploring free energy landscapes of chemical reactions. , 2006, Accounts of chemical research.
[469] Yingkai Zhang,et al. Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. , 2005, The Journal of chemical physics.
[470] Kristina Nilsson,et al. Quantum chemical geometry optimizations in proteins using crystallographic raw data , 2002, J. Comput. Chem..
[471] J. Bertrán,et al. A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution , 2000 .
[472] F. Neese,et al. Spectroscopic and computational evaluation of the structure of the high-spin Fe(IV)-oxo intermediates in taurine: alpha-ketoglutarate dioxygenase from Escherichia coli and its His99Ala ligand variant. , 2007, Journal of the American Chemical Society.
[473] U. Singh,et al. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .
[474] K. Schulten,et al. Energetics of glycerol conduction through aquaglyceroporin GlpF , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[475] A. Mulholland,et al. The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure. , 2006, Biophysical journal.
[476] A. Turner,et al. Transition-state structural refinement with GRACE and CHARMM: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method , 1997 .
[477] I. Tvaroška,et al. Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I. , 2006, Journal of the American Chemical Society.
[478] M. Tuckerman,et al. An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles , 2002 .
[479] Wei Yang,et al. A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate , 2006, Proteins.
[480] Mark S. Gordon,et al. Effective Fragment Method for Modeling Intermolecular Hydrogen-Bonding Effects on Quantum Mechanical Calculations , 1994 .
[481] J Andrew McCammon,et al. How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study , 2006, Protein science : a publication of the Protein Society.
[482] U. Ryde,et al. Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase , 2006 .
[483] Feliu Maseras,et al. The IMOMM method opens the way for the accurate calculation of “real” transition metal complexes , 2000 .
[484] H. Bernhard Schlegel,et al. Exploring potential energy surfaces for chemical reactions: An overview of some practical methods , 2003, J. Comput. Chem..
[485] Jiali Gao,et al. The Design of a Next Generation Force Field: The X-POL Potential. , 2007, Journal of chemical theory and computation.
[486] C. Dellago,et al. Transition path sampling and the calculation of rate constants , 1998 .
[487] Donald G Truhlar,et al. Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.
[488] S. C. Rogers,et al. QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .
[489] S. Dalosto. Computer simulation of the interaction of Cu(I) with cys residues at the binding site of the yeast metallochaperone Cu(I)-Atx1. , 2007, The journal of physical chemistry. B.
[490] B. Grigorenko,et al. Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling , 2007, Proceedings of the National Academy of Sciences.
[491] B. Grigorenko,et al. Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595. , 2006, The journal of physical chemistry. B.
[492] G. Murshudov,et al. The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations. , 2007, Journal of the American Chemical Society.
[493] J. Bertrán,et al. Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase , 2001 .
[494] H. Bernhard Schlegel,et al. Methods for optimizing large molecules. II. Quadratic search , 1999 .
[495] H. Bernhard Schlegel,et al. Geometry Optimization on Potential Energy Surfaces , 1995 .
[496] Qiang Cui,et al. pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications. , 2007, The journal of physical chemistry. A.
[497] Shawn T. Brown,et al. A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin , 2006 .
[498] George A. Kaminski,et al. Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry , 2004 .
[499] Walter Thiel,et al. The Importance of the Active Site Histidine for the Activity of Epoxide‐ or Aziridine‐Based Inhibitors of Cysteine Proteases , 2007, ChemMedChem.
[500] Leonardo Boechi,et al. Dioxygen affinity in heme proteins investigated by computer simulation. , 2006, Journal of inorganic biochemistry.
[501] Michel A Cuendet. Statistical mechanical derivation of Jarzynski's identity for thermostated non-Hamiltonian dynamics. , 2006, Physical review letters.
[502] Jiali Gao,et al. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials , 2007 .
[503] Alessandro Laio,et al. A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. , 2005, The journal of physical chemistry. B.
[504] Ivano Tavernelli,et al. Variational optimization of effective atom centered potentials for molecular properties. , 2005, The Journal of chemical physics.
[505] Martin J. Field,et al. Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method , 2003 .
[506] Ulf Ryde,et al. Combined quantum and molecular mechanics calculations on metalloproteins. , 2003, Current opinion in chemical biology.
[507] Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase , 2007, Proceedings of the National Academy of Sciences.
[508] Adrian J Mulholland,et al. Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate. , 2007, The journal of physical chemistry. B.
[509] M. Cascella,et al. A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. , 2004, Journal of the American Chemical Society.
[510] Xiaodong Zhang,et al. Catalytic mechanism and product specificity of rubisco large subunit methyltransferase: QM/MM and MD investigations. , 2007, Biochemistry.
[511] R. Friesner,et al. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .
[512] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[513] I. Tuñón,et al. Activation free energy of catechol O-methyltransferase. Corrections to the potential of mean force. , 2006, Journal of Physical Chemistry A.
[514] Qin Xu,et al. Stabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfers. , 2007, The journal of physical chemistry. B.
[515] D. Yamaki,et al. Simple minimum principle to derive a quantum-mechanical/molecular-mechanical method. , 2004, The Journal of chemical physics.
[516] Alexander Wlodawer,et al. The importance of dynamics in substrate-assisted catalysis and specificity. , 2006, Journal of the American Chemical Society.
[517] M. Boero,et al. Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction. , 2006, Journal of the American Chemical Society.
[518] Walter Thiel,et al. Combined Quantum Mechanical and Molecular Mechanical Approaches , 1998 .
[519] N. Ferré,et al. The amide bond: pitfalls and drawbacks of the link atom scheme , 2003 .
[520] Pedro Alexandrino Fernandes,et al. Determination of the ΔpKa between the active site cysteines of thioredoxin and DsbA , 2006, J. Comput. Chem..
[521] T. Ziegler,et al. Combined Car−Parrinello QM/MM Dynamic Study on the Propagation and Termination Steps of Ethylene Polymerization Catalyzed by [Cp2ZrR(μ-Me)B(C6F5)3] (R = Me, Pr) , 2006 .
[522] Ursula Rothlisberger,et al. Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations , 2004 .
[523] Arieh Warshel,et al. Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. , 2003, Journal of the American Chemical Society.
[524] Donald G Truhlar,et al. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. , 2006, Chemical reviews.
[525] Wei Yang,et al. On the convergence improvement in the metadynamics simulations: a Wang-Landau recursion approach. , 2007, The Journal of chemical physics.
[526] A. Warshel,et al. Electrostatic basis for enzyme catalysis. , 2006, Chemical reviews.
[527] S. Shaik,et al. Does substrate oxidation determine the regioselectivity of cyclohexene and propene oxidation by cytochrome p450? , 2006, Journal of the American Chemical Society.
[528] H. Nakatsuji,et al. Red light in chemiluminescence and yellow-green light in bioluminescence: color-tuning mechanism of firefly, Photinus pyralis, studied by the symmetry-adapted cluster-configuration interaction method. , 2007, Journal of the American Chemical Society.
[529] J. Platts,et al. Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study. , 2006, The journal of physical chemistry. A.
[530] Bernard R. Brooks,et al. Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics , 2002 .
[531] T. Clark,et al. Some Biological Applications of Semiempirical MO Theory , 2002 .
[532] Scott F. Smith,et al. SN2 reaction profiles in the gas phase and aqueous solution , 1984 .
[533] A. Fornili,et al. Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods , 2006 .
[534] A. Laio,et al. Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. , 2006, The journal of physical chemistry. B.
[535] Georg Hetzer,et al. Low-order scaling local electron correlation methods. I. Linear scaling local MP2 , 1999 .
[536] Suse Broyde,et al. A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. , 2007, Journal of the American Chemical Society.
[537] Walter Thiel,et al. Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates , 2000 .
[538] K. Schulten,et al. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality , 2003 .
[539] Martin J. Field,et al. The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives , 2000 .
[540] Toru Nakayama,et al. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As. , 2007, Biochemistry.
[541] K. Nam,et al. Transition State Stabilization and α-Amino Carbon Acidity in Alanine Racemase , 2006 .
[542] Arieh Warshel,et al. Polarizable Force Fields: History, Test Cases, and Prospects. , 2007, Journal of chemical theory and computation.
[543] Jing Kong,et al. Lennard–Jones parameters for the combined QM/MM method using the B3LYP/6‐31G*/AMBER potential , 2005, J. Comput. Chem..
[544] J. Mccammon,et al. Molecular dynamics with stochastic boundary conditions , 1982 .
[545] R. Friesner. Combined quantum and molecular mechanics (QM/MM). , 2004, Drug discovery today. Technologies.
[546] I. Tuñón,et al. Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues. , 2007, Bioorganic & medicinal chemistry.
[547] Kenneth M. Merz,et al. Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential , 1995 .
[548] W. Thiel,et al. Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches , 1996 .
[549] M. Field,et al. A hybrid potential reaction path and free energy study of the chorismate mutase reaction. , 2001, Journal of the American Chemical Society.
[550] Kenneth M. Merz,et al. An Examination of a Hartree-Fock/Molecular Mechanical Coupled Potential , 1995 .
[551] Johannes C. Hermann,et al. Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase , 2003 .
[552] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[553] Alessandra Magistrato,et al. Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[554] Alessandro Laio,et al. Reconstructing the density of states by history-dependent metadynamics. , 2004, Physical review letters.
[555] Wei Zhang,et al. Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides , 2006, J. Comput. Chem..
[556] Ahmet Altun,et al. Systematic QM/MM investigation of factors that affect the cytochrome P450‐catalyzed hydrogen abstraction of camphor , 2006, J. Comput. Chem..
[557] Ulf Ryde,et al. Quantum mechanical free energy barrier for an enzymatic reaction. , 2005, Physical review letters.
[558] N. Foloppe,et al. Mechanisms of reaction in cytochrome P450: Hydroxylation of camphor in P450cam. , 2006, Organic & biomolecular chemistry.
[559] A. Roitberg,et al. The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation. , 2006, Journal of the American Chemical Society.
[560] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[561] D. Truhlar,et al. Coupling of hydrogenic tunneling to active-site motion in the hydrogen radical transfer catalyzed by a coenzyme B12-dependent mutase , 2007, Proceedings of the National Academy of Sciences.
[562] Sergio Martí,et al. Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy. , 2005, The journal of physical chemistry. B.
[563] J. Vervoort,et al. Frontier orbital study on the 4-hydroxybenzoate-3-hydroxylase-dependent activity with benzoate derivatives. , 1992, European journal of biochemistry.
[564] Donald G Truhlar,et al. Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. , 2007, The journal of physical chemistry. A.
[565] Jiali Gao,et al. Solvent Effects on the Bond Length Alternation and Absorption Energy of Conjugated Compounds , 1997 .
[566] Kenneth M. Merz,et al. An examination of a density functional/molecular mechanical coupled potential , 1995, J. Comput. Chem..
[567] Bohdan Waszkowycz,et al. A combined quantum mechanical/molecular mechanical model of the potential energy surface of ester hydrolysis by the enzyme phospholipase A2 , 1991 .
[568] Marat Valiev,et al. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. , 2007 .
[569] Jun-Ya Hasegawa,et al. Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins. , 2007, Journal of chemical theory and computation.
[570] Supot Hannongbua,et al. Insight into analysis of interactions of saquinavir with HIV-1 protease in comparison between the wild-type and G48V and G48V/L90M mutants based on QM and QM/MM calculations. , 2007, Journal of molecular graphics & modelling.
[571] Christoph Dellago,et al. Transition path sampling: throwing ropes over mountains in the dark , 2000 .
[572] Jiali Gao,et al. Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. , 2007, Journal of the American Chemical Society.