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Rene J. Trabanino et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Does substrate oxidation determine the regioselectivity of cyclohexene and propene oxidation by cytochrome P450?
Shimrit Cohen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems
Mats H. M. Olsson et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)
Color tuning in rhodopsins:: The mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II
Michael Hoffmann et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods
Arianna Fornili et al.
CHEMICAL PHYSICS LETTERS (2006)
Modeling dioxygen binding to the non-heme iron-containing enzymes
A. V. Nemukhin et al.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2006)
The planar conformation of a strained proline ring: A QM/MM study
Serena Donnini et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis
Dimitri Antoniou et al.
CHEMICAL REVIEWS (2006)
Computational approaches: Reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency
Thomas C. Bruice
CHEMICAL REVIEWS (2006)
Mechanisms and free energies of enzymatic reactions
Jiali Gao et al.
CHEMICAL REVIEWS (2006)
Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions
Jingzhi Pu et al.
CHEMICAL REVIEWS (2006)
A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X) PRTases
Aline Thomas et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Electrostatic basis for enzyme catalysis
Arieh Warshel et al.
CHEMICAL REVIEWS (2006)
Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts
W. J. H. van Berkel et al.
JOURNAL OF BIOTECHNOLOGY (2006)
Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): A DFT and QM/MM study
Kazunari Yoshizawa et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
Yingkai Zhang
THEORETICAL CHEMISTRY ACCOUNTS (2006)
Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase
Haobo Guo et al.
BIOCHEMISTRY (2006)
Quantum chemical calculations of reduction potentials of AnO22+/AnO2+ (An = U, Np, Pu, Am) and Fe3+/Fe2+ couples
Satoru Tsushima et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
A QM/MM study of cisplatin-DNA oligonucleotides: From simple models to realistic systems
Arturo Robertazzi et al.
CHEMISTRY-A EUROPEAN JOURNAL (2006)
Role of Mg2+ and Ca2+ in DNA bending:: Evidence from an ONIOM-based QM-MM study of a DNA fragment
Neethu Sundaresan et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study
Rajeev Prabhakar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Molecular modeling the reaction mechanism of serine-carboxyl peptidases
Ksenia Bravaya et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins
Patrik R. Callis et al.
CHEMICAL PHYSICS (2006)
QM/MM models of the O2-evolving complex of photosystem II
Eduardo M. Sproviero et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement
Ning Yu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
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
Etienne Derat et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Transition state stabilization and α-amino carbon acidity in alanine racemase
Dan T. Major et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations
Orlando Acevedo et al.
JOURNAL OF ORGANIC CHEMISTRY (2006)
Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions
Jiayun Pang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
QM/MM study on the catalytic mechanism of benzene hydroxylation over Fe-ZSM-5
Yoshihito Shiota et al.
ORGANOMETALLICS (2006)
Structure of reduced and oxidized manganese superoxide dismutase:: A combined computational and experimental approach
Lubomir Rulisek et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
trans and cis Chrornophore structures in the kindling fluorescent protein asFP595
Bella Grigorenko et al.
CHEMICAL PHYSICS LETTERS (2006)
The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: A QM/MM study
Etienne Derat et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Determination of the ΔpKa between the active site cysteines of thioredoxin and DsbA
ATP Carvalho et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Classical polarization in hybrid QM/MM methods
Christopher J. R. Illingworth et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
The importance of dynamics in substrate-assisted catalysis and specificity
Qin Xu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Cope elimination: Elucidation of solvent effects from QM/MM simulations
Orlando Acevedo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism
Sonja M. Schwarzl et al.
BIOCHEMISTRY (2006)
Implicit versus explicit solvent in free energy calculations of enzyme catalysis:: Methyl transfer catalyzed by catechol O-methyltransferase
TH Rod et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Rapid freeze-quench ENDOR study of chloroperoxidase compound I: The site of the radical
SH Kim et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: Correlation between structural rearrangement and chemical shifts in the acylation process
T Ishida
BIOCHEMISTRY (2006)
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
Thom Vreven et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Dynamical contributions to enzyme catalysis: Critical tests of a popular hypothesis
Mats H. M. Olsson et al.
CHEMICAL REVIEWS (2006)
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
ZX Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Modeling of ligation-induced helix/loop displacements in myoglobin: Toward an understanding of hemoglobin allostery
V Guallar et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: A quantum mechanics/molecular mechanics approach
XD Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
The catalytic power of enzymes: Conformational selection or transition state stabilization?
J Giraldo et al.
FEBS LETTERS (2006)
Atomic description of an enzyme reaction dominated by proton tunneling
L Masgrau et al.
SCIENCE (2006)
Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach
A Tongraar et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein
C Corminboeuf et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
QM/MM study of electron addition on protein disulfide bonds
J Bergès et al.
CHEMICAL PHYSICS LETTERS (2006)
Catalytic mechanism of dopamine, β-monooxygenase mediated by Cu(III)-Oxo
K Yoshizawa et al.
INORGANIC CHEMISTRY (2006)
Dioxygen affinity in heme proteins investigated by computer simulation
Marcelo A. Marti et al.
JOURNAL OF INORGANIC BIOCHEMISTRY (2006)
Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases
Hans-Petter Hersleth et al.
JOURNAL OF INORGANIC BIOCHEMISTRY (2006)
Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis:: A hybrid QM/MM study
XF Gao et al.
JOURNAL OF STRUCTURAL BIOLOGY (2006)
How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study
YH Cheng et al.
PROTEIN SCIENCE (2006)
Catalytic mechanism of class B2 metallo-β-lactamase
DG Xu et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
Statistical mechanical derivation of Jarzynski's identity for thermostated non-Hamiltonian dynamics
MA Cuendet
PHYSICAL REVIEW LETTERS (2006)
A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
C Rovira et al.
CHEMICAL PHYSICS (2006)
The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis:: A QM/MM study
A Altun et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study
A Robertazzi et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Equilibrium free energies from nonequilibrium metadynamics
G Bussi et al.
PHYSICAL REVIEW LETTERS (2006)
Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: Insights from hybrid QM/MM molecular dynamics simulations
A Magistrato et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
P Raiteri et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Structure and function of vanadium haloperoxidases
S Raugei et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Duocarmycins binding to DNA investigated by molecular simulation
K Spiegel et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Geometry optimization with QM/MM methods II: Explicit quadratic coupling
T Vreven et al.
MOLECULAR PHYSICS (2006)
QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling:: Application to an enzymatic reaction
J Kästner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
YW Hslao et al.
INORGANICA CHIMICA ACTA (2006)
Computational studies of the primary phototransduction event in visual rhodopsin
JA Gascón et al.
ACCOUNTS OF CHEMICAL RESEARCH (2006)
On the suitability of strictly localized orbitals for hybrid QM/MM calculations
A Fornili et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
In silico design of a mutant of cytochrome p450 containing selenocysteine
S Cohen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Excited state intramolecular proton transfer in 1-(trifluoroacetylamino)naphthaquinone: a CASPT2//CASSCF computational study
A Cembran et al.
MOLECULAR PHYSICS (2006)
Multicentered valence electron effective potentials:: A solution to the link atom problem for ground and excited electronic states
P Slavícek et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Enantioselective palladium-catalyzed hydrosilylation of styrene: Influence of electronic and steric effects on enantioselectivity and catalyst design via hybrid QM/MM molecular dynamics simulations
A Magistrato et al.
ORGANOMETALLICS (2006)
A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin
M Freindorf et al.
CHEMICAL PHYSICS LETTERS (2006)
Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions
E Rosta et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
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)
SY Yang et al.
ORGANOMETALLICS (2006)
Explicitly correlated second-order perturbation theory using density fitting and local approximations
HJ Werner et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity
S Pieraccini et al.
CHEMICAL PHYSICS LETTERS (2006)
Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB - A quantum chemical analysis
YM Liu et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
The Fe-CO bond energy in myoglobin: A QM/MM study of the effect of tertiary structure
N Strickland et al.
BIOPHYSICAL JOURNAL (2006)
Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures
P Hu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Metadynamics as a tool for exploring free energy landscapes of chemical reactions
B Ensing et al.
ACCOUNTS OF CHEMICAL RESEARCH (2006)
Equilibrium free energies from fast-switching trajectories with large time steps
W Lechner et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction
T Ishida et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Binding of phosphinate and phosphonate inhibitors to aspartic proteases: A first-principles study
P Vidossich et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Origin and consequences of steric strain in the rhodopsin binding pocket
M Sugihara et al.
BIOCHEMISTRY (2006)
Molecular mechanisms of antibiotic resistance:: QM/MM modelling of deacylation in a class A β-lactamase
JC Hermann et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2006)
Substrate distortion in the michaelis complex of Bacillus 1,3-1,4-β-glucanase -: Insight from first principles molecular dynamics simulations
X Biarnés et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase
GA Cisneros et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
On the ionization state of the substrate in the active site of glutamate racemase.: A QM/MM study about the importance of being zwitterionic
E Puig et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Activation free energy of catechol O-methyltransferase.: Corrections to the potential of mean force
M Roca et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Structure and redox properties of the protein, rubredoxin, and its ligand and metal mutants studied by electronic structure calculation
M Sundararajan et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
A charge-scaling implementation of the variational electrostatic projection method
BA Gregersen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: A combined theoretical and experimental study
JB Wu et al.
BIOCHEMISTRY (2006)
H-X bond activation via hydrogen transfer to hydride in ruthenium N-heterocyclic carbene complexes: Density functional and synthetic studies
SL Chatwin et al.
ORGANOMETALLICS (2006)
Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase
DQ Gao et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam
Jolanta Zurek et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2006)
QM/MM modelling of the TS-1 catalyst using HPCx
Judy To et al.
JOURNAL OF MATERIALS CHEMISTRY (2006)
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
Sebastian Sinnecker et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2006)
Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations
Katrin Spiegel et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2006)
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
Konstantinos Paraskevopoulos et al.
DALTON TRANSACTIONS (2006)
Simulation of Co-59 NMR chemical shifts in aqueous solution
M Buhl et al.
CHEMISTRY-A EUROPEAN JOURNAL (2006)
High-accuracy computation of reaction barriers in enzymes
Frederik Claeyssens et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2006)
Structural and energetic determinants of primary proton transfer in bacteriorhodopsin
Ana-Nicoleta Bondar et al.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES (2006)
Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems (vol 1, pg 1008, 2005)
S Marti et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
The IMOMM (integrated molecular orbitals/molecular mechanics) approach for ligand-stabilized metal clusters. Comparison to full density functional calculations for the model thiolate cluster Cu-13(SCH2CH3)(8)
A Genest et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study
Sebastian Sinnecker et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2006)
Coordination and ligand exchange dynamics of solvated metal ions
BM Rode et al.
COORDINATION CHEMISTRY REVIEWS (2005)
Accounting for polarization in molecular simulation
HB Yu et al.
COMPUTER PHYSICS COMMUNICATIONS (2005)
Accurate QM/MM free energy calculations of enzyme reactions:: Methylation by catechol O-methyltransferase
TH Rod et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0
D Kumar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Modelling enzyme reaction mechanisms, specificity and catalysis
AJ Mulholland
DRUG DISCOVERY TODAY (2005)
Polarizable empirical force field for alkanes based on the classical drude oscillator model
IV Vorobyov et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
How enzyme dynamics helps catalyze a reaction in atomic detail: A transition path sampling study
JE Basner et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method:: umbrella integration -: art. no. 144104
J Kästner et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Principal active species of horseradish peroxidase, compound I: A hybrid quantum mechanical/molecular mechanical study
E Derat et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
pKa calculations in solution and proteins with QM/MM free energy perturbation simulations:: A quantitative test of QM/MM protocols
D Riccardi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling
CM Bathelt et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Two states and two more in the mechanisms of hydroxylation and epoxidation by cytochrome P450
H Hirao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals
JZ Pu et al.
CHEMPHYSCHEM (2005)
Improving the QM/MM description of chemical processes:: A dual level strategy to explore the potential energy surface in very large systems
S Martí et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31+G*/AMBER potential
M Freindorf et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions
M Klähn et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
A definitive mechanism for chorismate mutase
XD Zhang et al.
BIOCHEMISTRY (2005)
Water-assisted oxo mechanism for heme metabolism
T Kamachi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Unprejudiced identification of reaction mechanisms from biased transition path sampling
D Zahn
JOURNAL OF CHEMICAL PHYSICS (2005)
Dual-topology/dual-coordinate free-energy simulation using QM/MM force field
H Hu et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
P Schaefer et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Effects of Arg90 neutralization on the enzyme-catalyzed rearrangement of chorismate to prephenate
CRW Guimaraes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
QM/MM study of the NMR spectroscopy of the retinyl chromophore in visual rhodopsin
JA Gascón et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes
S Shaik et al.
CHEMICAL REVIEWS (2005)
Structure and chemistry of cytochrome P450
IG Denisov et al.
CHEMICAL REVIEWS (2005)
Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase
A Crespo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method
PH König et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations
H Lin et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2005)
Enzymatic hydroxylation in p-hydroxybenzoate hydroxylase:: A case study for QM/MM molecular dynamics
HM Senn et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Toward identification of the Compound I reactive intermediate in cytochrome P450 chemistry:: A QM/MM study of its EPR and Mossbauer parameters
JC Schöneboom et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Theoretical study of structure of catalytic copper site in nitrite reductase
N Källrot et al.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2005)
Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts
CRA Catlow et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2005)
A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions
B Ensing et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Assessing the accuracy of metadynamics
A Laio et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Quantum mechanical free energy barrier for an enzymatic reaction
TH Rod et al.
PHYSICAL REVIEW LETTERS (2005)
Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order chain-of-replicas methods
GA Cisneros et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Computing kinetic isotope effects for chorismate mutase with high accuracy.: A new DFT/MM strategy
S Martí et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Substrate binding in the active site of cytochrome P450cam
M Swart et al.
CHEMICAL PHYSICS LETTERS (2005)
NMR structure determination of proteins supplemented by quantum chemical calculations:: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
YW Hsiao et al.
JOURNAL OF BIOMOLECULAR NMR (2005)
Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes
A Altun et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Efficient silicon surface and cluster modeling using quantum capping potentials
GA DiLabio et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations
BA Gregersen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods -: art. no. 024114
YK Zhang
JOURNAL OF CHEMICAL PHYSICS (2005)
An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
K Nam et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator
VM Anisimov et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase
CM Bathelt et al.
DALTON TRANSACTIONS (2005)
Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization
F Claeyssens et al.
CHEMICAL COMMUNICATIONS (2005)
Variational optimization of effective atom centered potentials for molecular properties
OA von Lilienfeld et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Reconstructing the density of states by history-dependent metadynamics
C Micheletti et al.
PHYSICAL REVIEW LETTERS (2004)
Photoactivation of the photoactive yellow protein: Why photon absorption triggers a trans-to-cis lsomerization of the chromophore in the protein
G Groenhof et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Calculating potentials of mean force from steered molecular dynamics simulations
S Park et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam:: Theory supports a two-state rebound mechanism
JC Schöneboom et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method
M Garcia-Viloca et al.
THEORETICAL CHEMISTRY ACCOUNTS (2004)
Theoretical insights in enzyme catalysis
S Martí et al.
CHEMICAL SOCIETY REVIEWS (2004)
Biocatalytic potential of p-hydroxybenzoate hydroxylase from Rhodococcus rhodnii 135 and Rhodococcus opacus 557
AP Jadan et al.
ADVANCED SYNTHESIS & CATALYSIS (2004)
Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2004)
Generalized hybrid orbital (GHO) method for combining ab initio Hartree-Fock wave functions with molecular mechanics
JZ Pu et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2004)
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
S Patel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A comparative study of claisen and cope Rearrangements catalyzed by chorismate mutase.: An insight into enzymatic efficiency:: Transition state stabilization or substrate preorganization?
S Martí et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
How enzymes work: Analysis by modern rate theory and computer simulations
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