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Wang W., Donini O., Reyes C.M., Kollman P.A. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30:2001;211-243.
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Wang, W.1
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Villa J., Warshel A. Energetics and dynamics of enzymatic reactions. J. Phys. Chem. B. 105:2001;7887-7907.
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Villa, J.1
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0035977645
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A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme
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Garcia-Viloca M., González-Lafont À., Lluch J.M. A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme. J. Am. Chem. Soc. 123:2001;709-721.
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Garcia-Viloca, M.1
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Ab initio hybrid quantum mechanical/molecular mechanical studies of the mechanisms of the enzymes protein kinase and thymidine phosphorylase
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Sheppard D.W., Burton N.A., Hillier I.H. Ab initio hybrid quantum mechanical/molecular mechanical studies of the mechanisms of the enzymes protein kinase and thymidine phosphorylase. J. Mol. Struct. 506:2000;35-44.
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2: Semiempirical MO calculations including the protein environment
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2: semiempirical MO calculations including the protein environment. J. Phys. Chem. B. 104:2000;1349-1361.
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Insights in the peptide hydrolysis mechanism by thermolysin: A theoretical QM/MM study
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Antonczak S., Monard G., Ruiz-López M., Rivail J.-L. Insights in the peptide hydrolysis mechanism by thermolysin: a theoretical QM/MM study. J. Mol. Model. 6:2000;527-538.
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Antonczak, S.1
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The reaction mechanism of bovine lens leucine aminopeptidase
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Shürer G., Horn A.H.C., Gedeck P., Clark T. The reaction mechanism of bovine lens leucine aminopeptidase. J. Phys. Chem. B. 106:2002;8815-8830.
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Pelmenschikov V., Siegbahn P.E.M. Catalytic mechanism of matrix metalloproteinases: two-layered ONIOM study. Inorg. Chem. 41:2002;5659-5666.
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A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations
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Rothlisberger U., Carloni P., Doclo K., Parrinello M. A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations. J. Biol. Inorg. Chem. 5:2000;236-250.
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Alhambra C., Corchado J.C., Sánchez M.L., Gao J., Truhlar D.G. Quantum dynamics of hydride transfer in enzyme catalysis. J. Am. Chem. Soc. 122:2000;8197-8203.
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25
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0035892157
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Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunnelling dynamics. Theory and application to liver alcohol dehydrogenase
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Variational transition-state theory is used to study kinetic isotope effects and QM tunnelling in alcohol dehydrogenase using QM/MM semiempirical valence-bond and potential-of-mean-force calculations
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Alhambra C., Corchado J., Sánchez M.L., Garcia-Viloca M., Gao J., Truhlar D.G. Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunnelling dynamics. Theory and application to liver alcohol dehydrogenase. J. Phys. Chem. B. 105:2001;11326-11340 Variational transition-state theory is used to study kinetic isotope effects and QM tunnelling in alcohol dehydrogenase using QM/MM semiempirical valence-bond and potential-of-mean-force calculations.
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0037035975
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Calculations of hydrogen tunnelling and enzyme catalysis: A comparison of liver alcohol dehydrogenase, methylamine dehydrogenase and soybean lipoxygenase
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Tresandern G., McNamara J.P., Mohr M., Wang H., Burton N.A., Hillier I.H. Calculations of hydrogen tunnelling and enzyme catalysis: a comparison of liver alcohol dehydrogenase, methylamine dehydrogenase and soybean lipoxygenase. Chem. Phys. Lett. 258:2002;489-494.
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27
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0037076062
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A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH)
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A thorough study of proton and hydride transfer in alcohol dehydrogenase with the SCC-DFTB method combined with CHARMM. A perturbation approach is used to decide what residues are important for the reaction. Equilibrium effects of protein dynamics on the hydride transfer are studied by potential-of-mean-force calculations.
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Cui Q., Elstner M., Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). J. Phys. Chem. B. 106:2002;2721-2740 A thorough study of proton and hydride transfer in alcohol dehydrogenase with the SCC-DFTB method combined with CHARMM. A perturbation approach is used to decide what residues are important for the reaction. Equilibrium effects of protein dynamics on the hydride transfer are studied by potential-of-mean-force calculations.
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28
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0035625887
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Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: Modelling the covalent junction region and application to the enzyme xylose isomerase
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QM/MM study of kinetic isotope effects in xylose isomerase, but also an investigation of the effect of various treatments of the link region and quantum systems of various sizes.
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Nicoll R.M., Hindle S.A., MacKenzie G., Hillier I.H., Burton N.A. Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase. Theor. Chem. Acc. 106:2001;105-112 QM/MM study of kinetic isotope effects in xylose isomerase, but also an investigation of the effect of various treatments of the link region and quantum systems of various sizes.
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Nicoll, R.M.1
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0035812387
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Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides
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Hughes J.M., Hutter M.C., Reimers J.R., Hush N.S. Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides. J. Am. Chem. Soc. 123:2001;8550-8563.
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Swart M., van den Bosch M., Berendsen H.J.C., Canters G.W., Snijders J.G. Active site geometries of copper proteins obtained with a QM/MM approach. J. Inorg. Biochem. 86:2001;445.
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The importance of porphyrin distortions for the ferrochelatase reaction
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Comba P., Lledós A., Maseras F., Remenyi R. Hybrid quantum mechanics/molecular mechanics studies of the active site of the blue copper proteins amicyanin and rusticyanin. Inorg. Chim. Acta. 324:2001;21-26.
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Ryde U., Olsson M.H.M. Structure, strain, and reorganization energy of blue copper models in the protein. Intern. J. Quant. Chem. 81:2001;335-347.
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On the role of covalent strain in protein function
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Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase
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Torren M., Vreven T., Musaev D.G., Morokuma K. Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase. J. Am. Chem. Soc. 124:2001;192-193.
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0035926249
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Inner-sphere reorganisation energy of iron-sulphur clusters studied by theoretical methods
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Sigfridsson E., Olsson M.H.M., Ryde U. Inner-sphere reorganisation energy of iron-sulphur clusters studied by theoretical methods. Inorg. Chem. 40:2001;2509-2519.
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Quantum chemical geometry optimisations in proteins using crystallographic raw data
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This article presents a method to combine QM calculations and crystallographic refinement, thereby obtaining an optimum compromise between quantum chemistry and the crystallographic raw data. The method is applied to the binding of N-methylmesoporphyrin to ferrochelatase.
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Ryde U., Olsen L., Nilsson K. Quantum chemical geometry optimisations in proteins using crystallographic raw data. J. Comp. Chem. 23:2002;1058-1070 This article presents a method to combine QM calculations and crystallographic refinement, thereby obtaining an optimum compromise between quantum chemistry and the crystallographic raw data. The method is applied to the binding of N-methylmesoporphyrin to ferrochelatase.
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Ryde, U.1
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0034951055
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Influence of the haem pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: A QM/MM density functional study
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Rovira C., Schulze B., Eichinger M., Evenseck J., Parrinello M. Influence of the haem pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. Biophys. J. 81:2001;435-445.
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0034829463
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Molecular dynamics simulations of the mononuclear zinc-β-lactamase from Bacillus cereus
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Suáres D., Merz K.M. Molecular dynamics simulations of the mononuclear zinc-β-lactamase from Bacillus cereus. J. Am. Chem. Soc. 123:2001;3759-3770.
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0001664118
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A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
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Murphy R.B., Philipp D.M., Friesner R.A. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. J. Comp. Chem. 16:2000;1442-1457.
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Murphy, R.B.1
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44
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0037055032
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The elusive oxidant species of cytochrome P450 enzymes: Characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations
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This is an extended vacuum and QM/MM investigation of the geometric and electronic structure of compound I in cytochrome P450, showing an amazing sensitivity to the theoretical method.
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Schöneboom J.C., Lin H., Reuter N., Thiel W., Cohen S., Ogliaro F., Shaik S. The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. J. Am. Chem. Soc. 124:2002;8142-8151 This is an extended vacuum and QM/MM investigation of the geometric and electronic structure of compound I in cytochrome P450, showing an amazing sensitivity to the theoretical method.
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Schöneboom, J.C.1
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45
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0036051467
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Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions
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Colombo M.C., Guidoni L., Laio A., Magistrato A., Maurer P., Piana S., Roehrig U., Spiegel K., van de Vondele J., Zumstein M., Rothlisgerger U. Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions. Chimia. 56:2002;11-17.
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Colombo, M.C.1
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Spiegel, K.8
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46
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0034669776
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Molecular-dynamics simulations of the β domain of metallothionein with a semi-empirical treatment of the metal core
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Berweger C.D., Thiel W., van Gunsteren W.F. Molecular-dynamics simulations of the β domain of metallothionein with a semi-empirical treatment of the metal core. Proteins. 41:2000;299-315.
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Berweger, C.D.1
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N2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
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48
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0035155864
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Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: Quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution
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Kollman P.A., Kuhn B., Donini O., Perakyla M., Stanton R., Bakowies D. Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: Quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. Acc. Chem. Res. 34:2001;72-79.
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Kollman, P.A.1
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49
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0034686678
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How is the active site of enolase organized to catalyze two different reaction steps?
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2+ ions). Free energies along the reaction paths are obtained by free energy perturbations.
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2+ ions). Free energies along the reaction paths are obtained by free energy perturbations.
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Liu, H.1
Zhang, Y.2
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50
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0000556829
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A hybrid-potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction
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A study of the isomerisation of 2-aceto-2-hydroxybutyrate by acetohydroxy acid isomeroreductase. QM/MM calculations were performed at the AM1 method and the OPLS force field. The potential of mean force was calculated by umbrella sampling along a stipulated reaction coordinate.
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Proust-De Martin F., Dumas R., Field M.J. A hybrid-potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction. J. Am. Chem. Soc. 122:2000;7688-7697 A study of the isomerisation of 2-aceto-2-hydroxybutyrate by acetohydroxy acid isomeroreductase. QM/MM calculations were performed at the AM1 method and the OPLS force field. The potential of mean force was calculated by umbrella sampling along a stipulated reaction coordinate.
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J. Am. Chem. Soc.
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