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QM/MM Methods For Biomolecular Systems.

H. Senn, W. Thiel
Published 2009 · Chemistry, Medicine

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Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
This paper references
10.1021/JA0424732
Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters.
J. Schöneboom (2005)
10.1021/JA058196W
The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study.
Ahmet Altun (2006)
10.1039/B301875J
Theoretical insights in enzyme catalysis.
S. Martí (2004)
10.1021/ct700078b
Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology.
O. Acevedo (2007)
10.1021/JA070601R
Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses.
Y. Cheng (2007)
10.1002/prot.21228
Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras‐GAP proteins as rationalized by ab initio QM/MM simulations
B. Grigorenko (2007)
10.1016/J.CHEMPHYS.2005.08.049
A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
C. Rovira (2006)
10.1021/JP0632081
Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin.
Yoshiharu Sato (2006)
Soc
B. Waszkowycz (1268)
10.1016/S0014-5793(00)01844-5
Modelling flavin and substrate substituent effects on the activation barrier and rate of oxygen transfer by p‐hydroxybenzoate hydroxylase
L. Ridder (2000)
10.1021/JP0029109
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method
Q. Cui (2001)
10.1002/jcc.20446
QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase
J. Harvey (2006)
10.1021/BI060461I
Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase.
Haobo Guo (2006)
10.1063/1.1427722
Predicting unimolecular chemical reactions: Chemical flooding
E. M. Müller (2002)
10.1016/0009-2614(82)80028-6
Molecular dynamics with stochastic boundary conditions
M. Berkowitz (1982)
10.1142/9789812832108_0008
Geometry Optimization on Potential Energy Surfaces
H. Schlegel (1995)
Chem
R. J. Hall (1441)
10.1039/B508181E
Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization.
F. Claeyssens (2005)
10.1063/1.1691404
Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.
L. Xie (2004)
10.1021/JP0301103
Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry
George A. Kaminski (2004)
10.1021/JP0619181
Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.
R. Prabhakar (2006)
10.1007/3-540-69707-1_5
Hybrid Quantum Mechanics/Molecular Mechanics Methods in Transition Metal Chemistry
F. Maseras (1999)
10.1021/JP036755K
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics
J. Pu (2004)
10.1063/1.2801988
New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
Jaewoon Jung (2007)
10.1021/ct049844p
Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase:  A Case Study for QM/MM Molecular Dynamics.
H. Senn (2005)
10.1039/B505407A
QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase.
Christine M. Bathelt (2005)
Theory Comput
T. H. Rod (1251)
10.1021/JP0685986
Substrate orientation in 4-oxalocrotonate tautomerase and its effect on QM/MM energy profiles.
T. Tuttle (2007)
10.1021/CEN-V024N010.P1375
Molecular Architecture and Biological Reactions
L. Pauling (1946)
10.1016/S0166-1280(98)00475-8
A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES
S. Dapprich (1999)
10.1016/J.BPC.2006.09.013
A theoretical elucidation of bilirubin interaction with HSA's lysines: first electrostatic binding site in IIA subdomain.
Z. Moosavi-Movahedi (2007)
10.1021/JP063155N
Anthramycin-DNA binding explored by molecular simulations.
A. Vargiu (2006)
Theory Comput
Y.-L. Lin (1493)
10.1021/JA9700358
Solvent Effects on the Bond Length Alternation and Absorption Energy of Conjugated Compounds
Jiali Gao (1997)
10.1103/PHYSREVE.52.2893
Predicting slow structural transitions in macromolecular systems: Conformational flooding.
Grubmüller (1995)
10.1002/jcc.20577
Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere
S. F. Sousa (2007)
10.1002/CHEM.200700040
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
C. Alves (2007)
10.1021/JA061585L
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 (2006)
10.1007/0-306-47718-1_9
Enantioselective Hydrosilylation by Chiral Pd Based Homogeneous Catalysts with First- Principles and Combined QM/MM Molecular Dynamics Simulations
A. Magistrato (2002)
10.1021/ct6002687
Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins.
K. Fujimoto (2007)
10.1103/PHYSREVB.74.214101
EXAFS structure refinement supplemented by computational chemistry
Ya-Wen Hsiao (2006)
10.1021/JA036123B
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study.
V. Guallar (2004)
10.1021/JP991771W
Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods
I. Antes (1999)
10.1021/JP045424K
Assessing the accuracy of metadynamics.
A. Laio (2005)
10.1021/JP073864G
Inhibitor binding by metallo-beta-lactamase IMP-1 from Pseudomonas aeruginosa: quantum mechanical/molecular mechanical simulations.
C. Wang (2007)
10.1063/1.1772354
Simple minimum principle to derive a quantum-mechanical/molecular-mechanical method.
K. Yasuda (2004)
10.1063/1.2162874
Equilibrium free energies from fast-switching trajectories with large time steps.
W. Lechner (2006)
10.1021/JA0455143
A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations.
S. Raugei (2004)
10.1021/JP074858N
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.
C. Stanton (2007)
10.1063/1.1651473
Calculating potentials of mean force from steered molecular dynamics simulations.
S. Park (2004)
10.1063/1.2173992
Multicentered valence electron effective potentials: a solution to the link atom problem for ground and excited electronic states.
P. Slavíček (2006)
10.1007/S10858-004-6729-7
NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
Ya-Wen Hsiao (2005)
10.1023/B:TOCA.0000003087.47073.DE
Identification and Characterization of Active Sites and Their Catalytic Processes—the Cu/ZnO Methanol Catalyst
S. A. French (2003)
10.1021/JP022525E
Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies
Y. Zhang (2003)
10.1088/0953-8984/12/8A/316
Transition path sampling: Throwing ropes over mountains in the dark
P. Bolhuis (2000)
10.1126/SCIENCE.1126002
Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling
Laura Masgrau (2006)
Case in Protein Simulations (Adv
D.A.J.W. Ponder (2003)
10.1002/1096-987X(200009)21:12<1088::AID-JCC5>3.0.CO;2-8
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
Martin J. Field (2000)
10.1021/JA074222+
Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K.
Shuhua Ma (2007)
10.1016/J.JINORGBIO.2005.12.009
Dioxygen affinity in heme proteins investigated by computer simulation.
M. Martí (2006)
Chem
S. Sinnecker (1475)
10.1021/JP000887L
QM/MM Boundaries Across Covalent Bonds: A Frozen Localized Molecular Orbital-Based Approach for the Effective Fragment Potential Method
Visvaldas Kairys† and (2000)
10.1021/JP067898K
Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: oxidation of tryptamine by aromatic amine dehydrogenase.
Laura Masgrau (2007)
10.1021/JP057109J
Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
E. Rosta (2006)
10.1021/JP054261C
Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis.
Yuemin Liu (2006)
10.1021/JP054901B
Structure and function of vanadium haloperoxidases.
S. Raugei (2006)
10.1016/J.CPLETT.2006.04.055
trans and cis Chromophore structures in the kindling fluorescent protein asFP595
B. Grigorenko (2006)
10.1021/JP057295T
Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach.
L. Rulíšek (2006)
10.1002/jcc.20318
A charge‐scaling implementation of the variational electrostatic projection method
Brent A. Gregersen (2006)
10.1021/JP0442347
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method.
P. H. Koenig (2005)
10.1063/1.1308551
Geometry optimization of large biomolecules in redundant internal coordinates
B. Paizs (2000)
10.1142/9789812839664_0003
Finding transition pathways: throwing ropes over rough mountain passes, in the dark
David Chandler (1998)
10.1063/1.478083
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
Y. Zhang (1999)
Chem
J. Sauer (1493)
10.1021/JA061604R
Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): a DFT and QM/MM study.
K. Yoshizawa (2006)
Mulholland in Theoretical Biochemistry: Processes and Properties of Biological Systems (Theor
A J. (2001)
10.1039/B512969A
Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase.
J. C. Hermann (2006)
10.1080/00268970500417556
Excited state intramolecular proton transfer in 1-(trifluoroacetylamino)naphthaquinone: a CASPT2//CASSCF computational study
Alessandro Cembran (2006)
10.1063/1.475562
Transition path sampling and the calculation of rate constants
C. Dellago (1998)
10.1021/JP9913012
Zeolite structure and reactivity by combined quantum-chemical- classical calculations
A. D. Vries (1999)
10.1021/JA0357846
Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water, antibody, enzymes, and their mutants).
S. Hur (2003)
10.1021/JA00322A059
SN2 reaction profiles in the gas phase and aqueous solution
J. Chandrasekhar (1984)
10.1021/JP0636470
Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.
J. J. Ruiz-Pernía (2006)
10.1021/CR0503052
Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis.
D. Antoniou (2006)
10.1021/JA057523X
Cope elimination: elucidation of solvent effects from QM/MM simulations.
O. Acevedo (2006)
10.1016/J.CPLETT.2005.10.147
Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity
Stefano Pieraccini (2006)
10.1039/B516451F
Structural and energetic determinants of primary proton transfer in bacteriorhodopsin.
A. Bondar (2006)
10.1063/1.1370534
An efficient method for the coordinate transformation problem of massively three-dimensional networks
K. Németh (2001)
10.1021/JP068746S
Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies.
D. Xu (2007)
10.1002/JCC.540070604
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
U. C. Singh (1986)
10.1002/BIP.360240509
Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
C. Brooks (1985)
QM/MM Methods Angewandte Chemie
F. Claeyssens (2009)
10.1002/jcc.1156
Simulating enzyme reactions: Challenges and perspectives
M. Field (2002)
10.1021/JP001508R
Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method
Shigehiko Hayashi† and (2000)
10.1063/1.1757436
Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
Z. Lu (2004)
10.1021/BI051477W
Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study.
Jingbo Wu (2006)
10.1021/AR040198I
Metadynamics as a tool for exploring free energy landscapes of chemical reactions.
B. Ensing (2006)
10.1021/JP066256U
Proton transfer and associated molecular rearrangements in the photocycle of photoactive yellow protein: role of water molecular migration on the proton transfer reaction.
M. Kamiya (2007)
Chem
S. Hur (1473)
10.1021/ja076953f
Atomistic Approaches in Modern Biology: From Quantum Chemistry to Molecular Simulations. Topics in Current Chemistry, Volume 268 Edited by Markus Reiher (ETH Zürich). Springer: Berlin, Heidelberg, New York. 2007. xii + 362 pp. $329.00. ISBN 978-3-540-38082-5.
Robert Q. Topper (2007)
10.1021/JA064117K
Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction.
M. Boero (2006)
Chem
P. Hu (1278)
10.1021/JA066334R
A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase.
D. Major (2006)
10.1074/JBC.M507643200
Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations.
Xevi Biarnés (2006)
10.1073/pnas.1534873100
The near attack conformation approach to the study of the chorismate to prephenate reaction
S. Hur (2003)
10.1021/JA066847Y
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.
Ahmet Altun (2007)
10.1063/1.1290611
Linear scaling algorithm for the coordinate transformation problem of molecular geometry optimization
K. Németh (2000)
10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
N. Foloppe (2000)
10.1002/ANGE.200701348
Deprotonation Mechanism of NH4+ in the Escherichia coli Ammonium Transporter AmtB: Insight from QM and QM/MM Calculations†
Zexing Cao Prof. (2007)
10.1021/BI700119P
Catalytic mechanism and product specificity of rubisco large subunit methyltransferase: QM/MM and MD investigations.
X. Zhang (2007)
10.1017/S0033583500005333
Calculations of electrostatic interactions in biological systems and in solutions.
A. Warshel (1984)
10.1021/JA00287A028
Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
J. Chandrasekhar (1985)
10.1021/ct0501102
Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O-Methyltransferase.
T. H. Rod (2005)
10.1002/QUA.10555
Determination of Enzymatic Reaction Pathways Using QM/MM Methods
G. Monard (2003)
Theory Comput
P.-F. Loos (1053)
10.1002/QUA.20386
Theoretical study of structure of catalytic copper site in nitrite reductase
Niklas Källrot (2005)
10.1016/S0166-1280(00)00424-3
Towards solvation simulations with a combined ab initio molecular dynamics and molecular mechanics approach
T. Woo (2000)
10.1002/(SICI)1097-461X(1996)60:6<1189::AID-QUA7>3.0.CO;2-W
ENZYME MECHANISMS WITH HYBRID QUANTUM AND MOLECULAR MECHANICAL POTENTIALS.I. THEORETICAL CONSIDERATIONS
Kirsten P. Eurenius (1996)
10.1021/BK-1998-0712.CH008
A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation for Ab Initio Molecular Dynamics Simulations of Extended Systems
T. Woo (1998)
10.1021/JP071938I
Optical spectra of Cu(II)-azurin by hybrid TDDFT-molecular dynamics simulations.
M. Cascella (2007)
10.1021/JP049529Z
Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method
J. Pu (2004)
10.1021/JP9536514
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
D. Bakowies (1996)
Phys
C. Dellago (1977)
10.1007/S002140000153
The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives
P. Amara (2000)
10.1063/1.1462041
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
A. Laio (2002)
10.1021/JA066662R
Compound I of nitric oxide synthase: the active site protonation state.
K. Cho (2007)
10.1002/CHEM.200601466
Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase.
T. Kamachi (2007)
Theory Comput
P. L. Cummins (1211)
10.1063/1.472065
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−
Stéphane Humbel (1996)
10.1063/1.1738106
Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials.
Wei Yang (2004)
10.1146/ANNUREV.PHYSCHEM.55.091602.094410
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.
R. Friesner (2005)
10.1007/978-1-4020-3286-8_13
Hybrid Quantum Mechanics/ Molecular Mechanics Methods and their Application
M. Sierka (2005)
10.1002/jcc.10058
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method
N. Ferré (2002)
10.1021/CR0307143
Structure and chemistry of cytochrome P450.
I. Denisov (2005)
10.1063/1.1470497
Low-order scaling local electron correlation methods. V. Connected triples beyond (T): Linear scaling local CCSDT-1b
M. Schütz (2002)
10.1063/1.1950672
Unprejudiced identification of reaction mechanisms from biased transition path sampling.
D. Zahn (2005)
10.1021/CR050293K
Mechanisms and free energies of enzymatic reactions.
J. Gao (2006)
10.1039/B304550A
Linear scaling local coupled cluster theory with density fitting. Part I: 4-external integrals
M. Schütz (2003)
10.1021/JA060776L
Rapid freeze-quench ENDOR study of chloroperoxidase compound I: the site of the radical.
S. Kim (2006)
10.1021/BI061319K
Catalysis in glycine N-methyltransferase: testing the electrostatic stabilization and compression hypothesis.
A. Soriano (2006)
10.1103/PhysRevE.64.056101
Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.
F. Wang (2001)
10.1021/JA062954G
Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements.
U. Ryde (2007)
10.1074/jbc.M512517200
Catalytic Mechanism of Class B2 Metallo-β-lactamase*
D. Xu (2006)
10.1063/1.478397
Geometry optimization in delocalized internal coordinates: An efficient quadratically scaling algorithm for large molecules
J. Baker (1999)
10.1016/J.CPLETT.2006.10.011
On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study
K. Fujimoto (2006)
10.1021/JP060124J
Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.
B. Grigorenko (2006)
Phys
S. Humbel (1967)
Chem
F. Maseras (1179)
Chem
H. B. Schlegel (1527)
10.1021/J100181A009
Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials
J. Gao (1992)
10.1021/JP054276A
Structure and redox properties of the protein, rubredoxin, and its ligand and metal mutants studied by electronic structure calculation.
M. Sundararajan (2006)
10.1080/08927029008022130
Molecular Dynamics Simulations with Interaction Potentials Including Polarization Development of a Noniterative Method and Application to Water
T. Straatsma (1990)
Chem
J. Gao (1071)
10.1021/JP982115J
A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region
P. Lyne (1999)
10.1016/S0065-3233(03)66007-9
Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress.
A. Shurki (2003)
10.1021/JP062295U
Quantum chemical calculations of reduction potentials of AnO2(2+)/AnO2+ (An = U, Np, Pu, Am) and Fe3+/Fe2+ couples.
S. Tsushima (2006)
10.1021/JP054828P
Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations.
A. Magistrato (2006)
10.1016/j.febslet.2007.11.026
Role of the arginine finger in Ras·RasGAP revealed by QM/MM calculations
Henrik te Heesen (2007)
10.1021/JA056586C
In silico design of a mutant of cytochrome P450 containing selenocysteine.
S. Cohen (2006)
10.1021/jp074958t
Quantum and molecular mechanical study of the first proton transfer in the catalytic cycle of cytochrome P450cam and its mutant D251N.
Dongqi Wang (2008)
10.1063/1.476656
Transition pathways in a many-body system: Application to hydrogen-bond breaking in water
F. Csajka (1998)
10.1063/1.1353552
A “fast growth” method of computing free energy differences
D. Hendrix (2001)
10.1021/JA063660Y
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.
M. Alfonso-Prieto (2007)
10.1073/pnas.0610126104
Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase
Xiaodong Zhang (2007)
10.1063/1.477309
An efficient direct method for geometry optimization of large molecules in internal coordinates
B. Paizs (1998)
10.1021/ct7000107
Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations.
Y. Zhang (2007)
10.1073/pnas.0701727104
Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling
B. Grigorenko (2007)
10.1063/1.477393
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
Ö. Farkas (1998)
10.1021/BI0622827
Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase.
A. Bowman (2007)
10.1021/ct050252w
QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling:  Application to an Enzymatic Reaction.
J. Kästner (2006)
10.1063/1.1323265
Low-order scaling local electron correlation methods. III. Linear scaling local perturbative triples correction (T)
M. Schütz (2000)
10.1021/JP066689X
Computer simulation of the interaction of Cu(I) with cys residues at the binding site of the yeast metallochaperone Cu(I)-Atx1.
S. Dalosto (2007)
10.1529/BIOPHYSJ.107.108878
Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin.
M. Mroginski (2007)
10.1002/jcc.20082
Empirical force fields for biological macromolecules: Overview and issues
Alexander D. MacKerell (2004)
Chem
A. Altun (1337)
Chem
P. Vidossich (1442)
10.1016/J.JINORGBIO.2006.01.018
Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.
H. Hersleth (2006)
10.1016/J.CHEMPHYS.2006.01.039
Short range photoinduced electron transfer in proteins : QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins
P. Callis (2006)
10.1002/1521-3838(200207)21:2<119::AID-QSAR119>3.0.CO;2-B
Hybrid Car-Parrinello/molecular mechanics modelling of transition metal complexes: Structure, dynamics and reactivity
L. Guidoni (2002)
10.1021/JA065451J
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.
D. Riccardi (2006)
10.1103/PhysRevLett.78.2690
Nonequilibrium Equality for Free Energy Differences
C. Jarzynski (1997)
10.1021/CR050308E
Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.
J. Pu (2006)
10.1021/ct050289g
Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.
T. Vreven (2006)
10.1021/OM0509591
QM/MM Study on the Catalytic Mechanism of Benzene Hydroxylation over Fe-ZSM-5
Y. Shiota (2006)
10.1016/J.ICA.2005.11.036
Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
Ya-Wen Hsiao (2006)
10.1002/prot.21190
A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate
C. Oliva (2007)
10.1021/CR030722J
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes.
S. Shaik (2005)
10.1021/JP054555Y
On the ionization state of the substrate in the active site of glutamate racemase. A QM/MM study about the importance of being zwitterionic.
Eduard Puig (2006)
10.1021/JA039847W
Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism.
J. Schöneboom (2004)
10.1016/S1093-3263(99)00027-3
Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase.
L. Ridder (1999)
10.1002/QUA.10463
AddRemove: A new link model for use in QM/MM studies
M. Swart (2003)
10.1007/S00214-003-0512-9
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 (2004)
10.1021/JP0700130
Looking at self-consistent-charge density functional tight binding from a semiempirical perspective.
N. Otte (2007)
10.1007/S00214-002-0417-Z
A charge-scaling method to treat solvent in QM/MM simulations
A. Dinner (2003)
10.1002/jcc.20587
Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations
H. L. Woodcock (2007)
Computational Medicinal Chemistry for Drug Discovery
M.F.M. Engels (2004)
10.1002/QUA.21354
Quantum chemical analysis of reaction paths in chorismate mutase: Conformational effects and electrostatic stabilization
Borys Szefczyk (2007)
10.1021/JA0356481
Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization.
M. Strajbl (2003)
10.1007/978-94-010-0341-4_2
Application of the IMOMM (Integrated Molecular Orbital Molecular Mechanics) Method for Biopolymers
I. Komaromi (2002)
Theory Comput
Y. Zhang (1398)
10.1021/JA0620033
Heme protein oxygen affinity regulation exerted by proximal effects.
L. Capece (2006)
10.1021/JP0743469
Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate.
A. Rodríguez (2007)
10.1063/1.1940047
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.
P. Schaefer (2005)
Chem
N. Reuter (1735)
10.1002/jcc.20609
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase‐1
Ismael Tejero (2007)
thlisberger in Quantum Medicinal Chemistry (Methods Princ
D. Sebastiani (2003)
10.1002/(SICI)1096-987X(199706)18:8<1061::AID-JCC10>3.0.CO;2-G
Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model
Jiali Gao (1997)
10.1002/CHEM.200501566
A QM/MM study of cisplatin-DNA oligonucleotides: from simple models to realistic systems.
Arturo Robertazzi (2006)
10.1103/PhysRevLett.86.2050
Efficient, multiple-range random walk algorithm to calculate the density of states.
F. Wang (2001)
10.1002/jcc.20077
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
Sandeep Patel (2004)
10.1002/CHEM.200700044
Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase.
M. De Vivo (2007)
Computational Modeling of Homogeneous Catalysis (Catalysis by Metal Complexes
A. Magistrato (2002)
Chem
H. L. Woodcock (1502)
10.1063/1.2768343
Hybrid approach for free energy calculations with high-level methods: application to the SN2 reaction of CHCl3 and OH- in water.
M. Valiev (2007)
10.1007/S002140000203
Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase
S. Martí (2001)
10.1021/JP036236H
A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase
Alejandro Crespo (2003)
10.1021/BI060988V
Mechanism of the highly efficient quenching of tryptophan fluorescence in human gammaD-crystallin.
J. Chen (2006)
10.1002/jcc.20386
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
Z. Wang (2006)
10.1021/JP0446332
Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.
H. Lin (2005)
10.1039/B211473A
Some critical issues in the application of quantum mechanics/molecular mechanics methods to the study of transition metal complexes.
David Balcells (2003)
10.1063/1.478569
On the calculation of reaction rate constants in the transition path ensemble
C. Dellago (1999)
10.1073/pnas.202427399
Escaping free-energy minima
A. Laio (2002)
10.1021/JA072532M
Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies.
D. Xu (2007)
10.1007/S002140000247
Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase
R. Mark Nicoll (2001)
10.1007/S002140050391
Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations
T. Woo (1998)
10.1016/J.CCR.2005.03.032
Coordination and ligand exchange dynamics of solvated metal ions
B. Rode (2005)
10.1021/ct600313b
Calculation of a Complete Enzymic Reaction Surface:  Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase.
P. L. Cummins (2007)
10.1021/JP0268718
Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics
Y. Lee (2002)
10.1002/jcc.10156
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
T. Vreven (2003)
Phys
P. N. Day (1986)
10.1021/JA980639R
CORRELATION OF CALCULATED ACTIVATION ENERGIES WITH EXPERIMENTAL RATE CONSTANTS FOR AN ENZYME CATALYZED AROMATIC HYDROXYLATION
L. Ridder (1998)
10.1063/1.478043
Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
J. Banks (1999)
10.1021/jp037992q
Importance of van der Waals Interactions in QM/MM Simulations.
D. Riccardi (2004)
10.1073/PNAS.0601587103
The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach.
X. Zhang (2006)
Bersuker in Computational Chemistry: Reviews of Current Trends, Vol. 6 (Ed.
I B. (2001)
Theory Comput
J. Blumberger (1850)
10.1021/JP054359R
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.
P. Raiteri (2006)
Computational Biochemistry and Biophysics (Eds.
A. D. MacKerell (2001)
10.1021/BK-1998-0712.CH015
The Local Self-Consistent Field Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems
X. Assfeld (1998)
10.1039/P29910001819
A quantum mechanical/molecular mechanical model of inhibition of the enzyme phospholipase A2
B. Waszkowycz (1991)
10.1021/JP068657F
Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study.
C. Xiao (2007)
10.1021/jp7104709
Combined quantum mechanical and molecular mechanics studies of the electron-transfer reactions involving carbon tetrachloride in solution.
M. Valiev (2008)
10.1016/S0166-1280(01)00755-2
A QM/MM approach with effective fragment potentials applied to the dipeptide–water structures
A. Nemukhin (2002)
10.1063/1.480484
Methods for optimizing large molecules. II. Quadratic search
Ö. Farkas (1999)
10.1021/JA051912+
Water-assisted oxo mechanism for heme metabolism.
T. Kamachi (2005)
10.1063/1.468398
Dynamical fluctuating charge force fields: Application to liquid water
S. W. Rick (1994)
10.1126/SCIENCE.1088172
How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations
Mireia Garcia-Viloca (2004)
Chem
M. J. Field (1100)
10.1002/CPHC.200600304
On the influence of the local environment on the CO stretching frequencies in native myoglobin: assignment of the B-states in MbCO.
M. Meuwly (2006)
10.1002/prot.20713
Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase
D. Gao (2006)
10.1039/B601089J
QM/MM modelling of the TS-1 catalyst using HPCx
Judy To (2006)
10.1021/BI700460C
The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations.
Kin-Yiu Wong (2007)
10.1002/1096-987X(200012)21:16<1433::AID-JCC2>3.0.CO;2-P
Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase
R. J. Hall (2000)
10.1016/S0009-2614(96)01165-7
Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method
X. Assfeld (1996)
Chem
S. F. Sousa (1168)
10.1021/JA0611691
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.
N. Nakatani (2007)
10.1021/CR050283J
Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency.
T. C. Bruice (2006)
10.1021/JA057318H
Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.
V. Guallar (2006)
10.1002/jcc.10231
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods
H. Schlegel (2003)
10.1021/ct0501396
Improving the QM/MM Description of Chemical Processes:  A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems.
S. Martí (2005)
10.1002/(SICI)1097-461X(1996)58:2<153::AID-QUA4>3.0.CO;2-X
HYBRID CLASSICAL QUANTUM FORCE FIELD FOR MODELING VERY LARGE MOLECULES
G. Monard (1996)
Combined Quantum Mechanical and Molecular Mechanical Approaches
Tiziana Mordasini (1998)
10.1021/ct700296x
Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations:  Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems.
Y. Zhang (2008)
10.1063/1.1990113
Dual-topology/dual-coordinate free-energy simulation using QM/MM force field.
H. Hu (2005)
10.1021/JA072245I
Versatility of the electronic structure of compound I in catalase-peroxidases.
Pietro Vidossich (2007)
10.1021/ct7000792
Peptide Hydrolysis in Thermolysin:  Ab Initio QM/MM Investigation of the Glu143-Assisted Water Addition Mechanism.
J. Blumberger (2007)
10.1098/rstb.2006.1880
Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems
M. H. Olsson (2006)
10.1021/JA0210648
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.
S. Hur (2003)
10.1021/BI052433Q
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism.
S. Schwarzl (2006)
10.1103/PHYSREVLETT.90.238302
Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.
M. Iannuzzi (2003)
10.1021/JA065863S
Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations.
Ivan Tubert-Brohman (2006)
10.1021/JA00150A037
Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction
P. Lyne (1995)
10.1021/JP9717296
A Combined Car−Parrinello QM/MM Implementation for ab Initio Molecular Dynamics Simulations of Extended Systems: Application to Transition Metal Catalysis
T. Woo (1997)
10.1021/JP0714217
Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms.
H. L. Woodcock (2007)
10.1021/JP054754H
New features in the catalytic cycle of cytochrome P450 during the formation of compound I from compound 0.
D. Kumar (2005)
10.1103/PhysRevLett.96.090601
Equilibrium free energies from nonequilibrium metadynamics.
G. Bussi (2006)
10.1529/BIOPHYSJ.106.086835
Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations.
Y. Xiong (2006)
Chem
A. Altun (1280)
10.1016/J.CPLETT.2005.11.111
A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin
M. Freindorf (2006)
10.1007/S00214-002-0418-Y
Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method
T. Vreven (2003)
10.1021/J100017A017
Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization
M. Thompson (1995)
10.1110/ps.051852306
How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study
Y. Cheng (2006)
10.1021/JP0744883
Ab initio prediction of tryptophan fluorescence quenching by protein electric field enabled electron transfer.
P. Callis (2007)
10.1021/JA0534046
Principal active species of horseradish peroxidase, compound I: a hybrid quantum mechanical/molecular mechanical study.
E. Derat (2005)
10.1021/JP065947N
Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure.
M. Rogacheva (2007)
Biochem
K. Nilsson (1546)
10.1021/JP013346K
Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces
J. VandeVondele (2002)
10.1039/B513942B
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.
K. Paraskevopoulos (2006)
10.1126/SCIENCE.1056991
Autoionization in Liquid Water
P. Geissler (2001)
10.1021/JP012017P
Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?
P. Kollman (2002)
10.1021/BI051515B
Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process.
Toyokazu Ishida (2006)
10.1063/1.1527010
A discrete solvent reaction field model within density functional theory
L. Jensen (2003)
10.1063/1.1759318
Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.
H. Liu (2004)
10.1073/pnas.141230998
Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism
H. Guo (2001)
10.1002/CPHC.200700143
Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase.
K. E. Ranaghan (2007)
10.1039/B402388A
Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase.
K. E. Ranaghan (2004)
10.1021/JP0673056
Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study.
Lishan Yao (2007)
10.1063/1.1839857
Efficient silicon surface and cluster modeling using quantum capping potentials.
G. A. DiLabio (2005)
10.1021/JP049596T
The resting state of p450cam A QM/MM study
J. Schöneboom (2004)
10.1021/JA003522N
A hybrid potential reaction path and free energy study of the chorismate mutase reaction.
S. Marti (2001)
Classical and Quantum Dynamics in Condensed Phase Simulations (Eds.
D. Chandler (1998)
10.1021/JP0517192
pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
D. Riccardi (2005)
10.1021/JA060823+
A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.
A. Thomas (2006)
10.1021/JM051132B
In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions.
S. Senapati (2006)
10.1063/1.2150817
Explicitly correlated second-order perturbation theory using density fitting and local approximations.
H. Werner (2006)
10.1021/OM050246I
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 (2006)
10.1039/B006249I
The IMOMM method opens the way for the accurate calculation of “real” transition metal complexes
F. Maseras (2000)
10.1002/jcc.20559
Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations
R. Walker (2007)
Computer Modeling of Chemical Reactions in Enzymes and Solutions
A. Warshel (1991)
10.1016/j.jinorgbio.2007.11.006
Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin.
M. Freindorf (2008)
10.1103/PHYSREVLETT.94.138302
Quantum mechanical free energy barrier for an enzymatic reaction.
T. H. Rod (2005)
10.1002/jcc.20264
Lennard–Jones parameters for the combined QM/MM method using the B3LYP/6‐31G*/AMBER potential
M. Freindorf (2005)
10.1007/S00214-002-0413-3
Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method
P. Amara (2003)
10.1021/ct800193a
Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians.
Tobias Benighaus (2008)
10.2533/000942902777680865
Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions
M. Colombo (2002)
10.1021/JP026464W
Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments
B. Grigorenko (2002)
10.1021/IC062320A
A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases.
C. Greco (2007)
10.1063/1.2052648
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".
J. Kästner (2005)
10.1063/1.1829051
Variational optimization of effective atom centered potentials for molecular properties.
O. A. von Lilienfeld (2005)
Theory Comput
W. Xie (1900)
Drug Discovery Des
B. Beck (1998)
10.1002/jcc.20366
On the suitability of strictly localized orbitals for hybrid QM/MM calculations
A. Fornili (2006)
10.1002/0471433519.CH3
Potentials and Algorithms for Incorporating Polarizability in Computer Simulations
S. W. Rick (2003)
10.1016/j.ddtec.2004.11.008
Combined quantum and molecular mechanics (QM/MM).
R. Friesner (2004)
10.1021/JP076401J
QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding.
Dan Fishelovitch (2007)
10.1016/j.febslet.2006.03.060
The catalytic power of enzymes: Conformational selection or transition state stabilization?
J. Giraldo (2006)
10.1073/pnas.0702981104
Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
Hao-Bo Guo (2007)
10.1021/JA9621760
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
W. Jorgensen (1996)
10.1016/S0166-1280(03)00299-9
Conformational equilibrium of chorismate. A QM/MM theoretical study combining statistical simulations and geometry optimisations in gas phase and in aqueous solution
S. Martí (2003)
10.1039/P29900001259
A theoretical study of hydrolysis by phospholipase A2: the catalytic role of the active site and substrate specificity
B. Waszkowycz (1990)
10.1063/1.2186635
Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase.
T. H. Rod (2006)
10.1021/bk-1998-0712.ch001
Quantum Mechanical-Molecular Mechanical Coupled Potentials
K. Merz (1998)
10.1007/978-1-4020-3286-8_79
Transition Path Sampling
C. Dellago (2005)
10.1021/JP071526+
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.
S. Bhattacharyya (2007)
10.1021/JA00052A054
Mechanism of the human carbonic anhydrase II-catalyzed hydration of carbon dioxide
Y. J. Zheng (1992)
10.1002/cmdc.200600159
The Importance of the Active Site Histidine for the Activity of Epoxide‐ or Aziridine‐Based Inhibitors of Cysteine Proteases
Milena Mladenović (2007)
Phys
Y. Wu (1200)
10.1021/JP012658K
Enzymatic reactions of triosephosphate isomerase: A theoretical calibration study
C. Lennartz (2002)
10.1021/OM0507427
H-X bond activation via hydrogen transfer to hydride in ruthenium N-heterocyclic carbene complexes : Density functional and synthetic studies
Sarah L. Chatwin (2006)
10.1021/JA068821C
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.
L. Wang (2007)
10.1002/jcc.540140205
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
F. Lee (1993)
10.1039/B009011P
Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase
S. Billeter (2001)
10.1021/JP9924124
Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches
N. Reuter (2000)
10.1021/JP026213N
Ab initio QM/MM modeling of the hydroxylation step in p-hydroxybenzoate hydroxylase
L. Ridder (2003)
10.1002/jcc.10127
Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations
Pengyu Y. Ren (2002)
10.1021/IC701051H
Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide.
C. Greco (2007)
10.1016/S1380-7323(01)80015-7
The QM/MM Approach to Enzymatic Reactions
A. Mulholland (2001)
10.1002/CHEM.200700295
51V NMR chemical shifts calculated from QM/MM models of vanadium chloroperoxidase.
M. Waller (2007)
Chem
J. N. Harvey (1362)
10.1023/A:1027259921634
Some Biological Applications of Semiempirical MO Theory
B. Beck (2002)
10.1039/P29910000225
A combined quantum mechanical/molecular mechanical model of the potential energy surface of ester hydrolysis by the enzyme phospholipase A2
B. Waszkowycz (1991)
10.1039/B108658H
Methods for optimizing large molecules. Part III. An improved algorithm for geometry optimization using direct inversion in the iterative subspace (GDIIS)
Ö. Farkas (2002)
10.1007/BF00124016
Local elevation: A method for improving the searching properties of molecular dynamics simulation
T. Huber (1994)
10.1002/ANIE.200219878
Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations.
H. Guo (2003)
10.1021/ct0500803
Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate.
C. Guimarães (2005)
10.1021/CR0503106
Electrostatic basis for enzyme catalysis.
A. Warshel (2006)
10.1021/JA0293047
Enzymes do what is expected (chalcone isomerase versus chorismate mutase).
S. Hur (2003)
10.1007/S00214-006-0200-7
Extremely localized molecular orbitals: theory and applications
M. Sironi (2007)
Combined Quantum Mechanical and Molecular Mechanical Methods
P. V. Duijnen (1999)
10.1063/1.480503
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
Y. Zhang (2000)
10.1021/JP061774Q
Role of Mg2+ and Ca2+ in DNA bending: evidence from an ONIOM-based QM-MM study of a DNA fragment.
Neethu Sundaresan (2006)
10.1063/1.1564816
Fast linear scaling second-order Møller-Plesset perturbation theory (MP2) using local and density fitting approximations
H. Werner (2003)
10.1021/JA043320H
How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study.
Jodi Basner (2005)
10.1021/JP057144Q
Exploring the molecular mechanism for color distinction in humans.
R. Trabanino (2006)
10.1021/JP001888G
A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution
S. Martí (2000)
10.1021/JO060533B
Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations.
O. Acevedo (2006)
10.1021/ct700058c
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.
Lin (2007)
10.1016/J.CPLETT.2004.12.092
Substrate binding in the active site of cytochrome P450cam
M. Swart (2005)
Chem
R. B. Murphy (1457)
10.1007/S00214-001-0308-8
The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface
X. Prat-Resina (2002)
10.1021/JP037651C
Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations
S. Piana (2004)
10.1039/B210508J
QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.
S. Martí (2003)
10.1007/S00214-002-0421-3
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase
H. Lee Woodcock (2003)
10.1021/ct700127w
Polarizable Force Fields:  History, Test Cases, and Prospects.
A. Warshel (2007)
10.1002/CHEM.200601136
Latrunculin analogues with improved biological profiles by "diverted total synthesis": preparation, evaluation, and computational analysis.
A. Fürstner (2007)
10.1021/JA063269C
Does substrate oxidation determine the regioselectivity of cyclohexene and propene oxidation by cytochrome p450?
S. Cohen (2006)
10.1002/ANIE.200701348
Deprotonation mechanism of NH4+ in the Escherichia coli ammonium transporter AmtB: insight from QM and QM/MM calculations.
Z. Cao (2007)
10.1021/JP002747H
The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry
M. Gordon (2001)
10.1039/A702600E
Transition-state structural refinement with GRACE and CHARMM: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method
Vicente Moliner (1997)
10.1021/ct060018l
QM/MM Models of the O2-Evolving Complex of Photosystem II.
E. Sproviero (2006)
10.1063/1.474398
A combined method for determining reaction paths, minima, and transition state geometries
P. Y. Ayala (1997)
10.2174/1568026033452005
Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity.
L. Ridder (2003)
10.1021/ct6002753
Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations.
O. Acevedo (2007)
10.1039/A701790A
Computer simulation of zeolite structure and reactivity using embedded cluster methods
P. Sherwood (1997)
10.1002/jcc.10309
Flexible effective fragment QM/MM method: Validation through the challenging tests
A. Nemukhin (2003)
10.1039/B611653A
Mechanisms of reaction in cytochrome P450: Hydroxylation of camphor in P450cam.
J. Żurek (2006)
10.1021/BK-1998-0712.CH002
Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution
Jörg Bentzien (1998)
10.1021/JA00260A028
Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential
P. Bash (1987)
10.1021/JA058831Y
The importance of dynamics in substrate-assisted catalysis and specificity.
Q. Xu (2006)
10.1021/JP0544639
Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study.
Pietro Vidossich (2006)
10.1007/S00214-005-0008-X
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
Y. Zhang (2006)
10.1016/J.STR.2006.06.017
PcrA helicase, a prototype ATP-driven molecular motor.
Markus Dittrich (2006)
10.1021/JP067147I
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.
S. Wang (2007)
10.1016/S0009-2614(00)00066-X
Local perturbative triples correction (T) with linear cost scaling
M. Schütz (2000)
10.1063/1.1448491
On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
Lula Rosso (2002)
10.1016/J.JMGM.2007.04.002
Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase.
Marc W. van der Kamp (2007)
10.1021/BI7014579
Histone lysine methyltransferase SET7/9: formation of a water channel precedes each methyl transfer.
X. Zhang (2007)
Chem
Y. Liu (1381)
10.1002/JCC.540110605
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
M. Field (1990)
10.1021/JA071720+
Enzymatic effects on reactant and transition states. The case of chalcone isomerase.
J. J. Ruiz-Pernía (2007)
10.1002/jcc.10125
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
George A. Kaminski (2002)
10.1039/A808364I
Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase
A. J. Turner (1999)
10.1063/1.438959
Reaction path Hamiltonian for polyatomic molecules
W. Miller (1980)
Chem
A. V. Nemukhin (1420)
Chem
M. Freindorf (1278)
10.1021/CT600240Y
QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.
H. Hu (2007)
QM/MM Methods Angewandte Chemie
C. Greco (2007)
10.1021/AR950140R
Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
Jiali Gao (1996)
10.1021/AR970218Z
Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems
G. Monard (1999)
10.1021/JP064301S
A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase.
Lishan Yao (2006)
10.1002/CHEM.200500285
Simulation of 59Co NMR chemical shifts in aqueous solution.
M. Bühl (2005)
10.1063/1.1590311
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
S. Park (2003)
10.1021/JP0143138
D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations
A. Laio (2002)
10.1021/CR040427E
Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis.
M. H. Olsson (2006)
Phys
F. S. Csajka (1133)
10.1016/J.JMGM.2006.09.004
Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex.
T. Rungrotmongkol (2007)
10.1002/jcc.540160110
An examination of a density functional/molecular mechanical coupled potential
R. Stanton (1995)
10.1126/SCIENCE.312.5780.1600A
Show Me the Dog
F. Kleinhans (2006)
Theory Comput
T. Benighaus (1609)
10.1016/S0166-1280(03)00304-X
Quantum refinement - a combination of quantum chemistry and protein crystallography.
U. Ryde (2003)
10.1021/jp802092w
Multireference ab initio quantum mechanics/molecular mechanics study on intermediates in the catalytic cycle of cytochrome P450(cam).
Ahmet Altun (2008)
10.1021/JA053847+
Two states and two more in the mechanisms of hydroxylation and epoxidation by cytochrome P450.
H. Hirao (2005)
Warshel in Protein Simulations (Adv
A. A. Shurki (2003)
10.1021/JA065944O
Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I.
Stanislav Kozmon (2006)
10.1002/jcc.20426
QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study
S. Sinnecker (2006)
Theory Comput
O. Acevedo (1419)
10.1002/jcc.20701
Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies
Jingjing Zheng (2007)
10.1016/J.JBIOTEC.2006.03.044
Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts.
W. V. van Berkel (2006)
10.1021/JA0732126
An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.
K. Bravaya (2007)
10.1021/JP0557159
All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction.
Toyokazu Ishida (2006)
10.1529/BIOPHYSJ.106.091512
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.
Jans H. Alzate-Morales (2007)
10.1021/J100048A006
An Examination of a Hartree-Fock/Molecular Mechanical Coupled Potential
R. Stanton (1995)
10.1002/1096-987X(200012)21:16<1442::AID-JCC3>3.0.CO;2-O
A mixed quantum mechanics/molecular mechanics (QM/MM) method for large‐scale modeling of chemistry in protein environments
R. B. Murphy (2000)
10.1063/1.479957
Low-order scaling local electron correlation methods. I. Linear scaling local MP2
M. Schütz (1999)
10.1021/JA063439L
QM/MM study of mechanisms for compound I formation in the catalytic cycle of cytochrome P450cam.
J. Zheng (2006)
10.1146/annurev.physchem.59.032607.093618
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.
H. Hu (2008)
10.1002/CHEM.200390121
Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.
S. Martí (2003)
10.1002/jcc.10349
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
Y. Duan (2003)
10.1063/1.2731769
On the convergence improvement in the metadynamics simulations: a Wang-Landau recursion approach.
Donghong Min (2007)
10.1002/jcc.540150303
Quantum mechanical computations on very large molecular systems: The local self‐consistent field method
V. Théry (1994)
10.1063/1.2774980
Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.
C. Xiao (2007)
10.1021/JP046944I
Classical polarization in hybrid QM/MM methods.
C. J. Illingworth (2006)
10.1002/jcc.20404
Determination of the ΔpKa between the active site cysteines of thioredoxin and DsbA
Alexandra T. P. Carvalho (2006)
10.1016/S0009-2614(00)00289-X
Frozen orbital QM/MM methods for density functional theory
R. B. Murphy (2000)
10.1021/JP984217F
The GROMOS biomolecular simulation program package
W. R. Scott (1999)
10.1021/JP074853Q
Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations.
M. Valiev (2007)
10.1103/PHYSREVLETT.55.2471
Unified approach for molecular dynamics and density-functional theory.
Car (1985)
10.1021/JA076108X
Structural characterization of the fleeting ferric peroxo species in myoglobin: experiment and theory.
M. Unno (2007)
10.1002/prot.21006
The planar conformation of a strained proline ring: A QM/MM study
Serena Donnini (2006)
10.1021/ct7000123
Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen:  The Effect of Explicitly Including Solvent Polarization.
D. Geerke (2007)
10.1016/0009-2614(84)80098-6
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
A. T. Brunger (1984)
10.1002/QUA.20072
Geometry optimization and transition state search in enzymes: Different options in the microiterative method
X. Prat-Resina (2004)
10.1021/CT0600060
Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement.
N. Yu (2006)
10.1021/JA056153+
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 (2006)
10.1063/1.476900
Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent
R. Bryce (1998)
10.1021/ct6003214
Self-Consistent Strictly Localized Orbitals.
P. Loos (2007)
10.1103/PhysRevE.56.5018
Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
C. Jarzynski (1997)
10.1021/BI700555G
Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations.
T. Wymore (2007)
10.1021/JA0365328
Quantum chemistry can locally improve protein crystal structures.
U. Ryde (2003)
10.1016/J.CPLETT.2006.01.052
QM/MM study of electron addition on protein disulfide bonds
J. Bergès (2006)
10.1021/JA0600734
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.
E. Derat (2006)
10.1021/BI050886P
A definitive mechanism for chorismate mutase.
X. Zhang (2005)
10.1002/QUA.21123
Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics
P. Lin (2006)
10.1016/J.CPLETT.2006.06.095
Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods
A. Fornili (2006)
10.1039/B612568A
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.
S. Sinnecker (2006)
10.1016/S0166-1280(03)00289-6
The amide bond: pitfalls and drawbacks of the link atom scheme
N. Ferré (2003)
10.1103/PHYSREVLETT.96.120602
Statistical mechanical derivation of Jarzynski's identity for thermostated non-Hamiltonian dynamics.
M. Cuendet (2006)
10.1021/JP0521757
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.
Marco Klähn (2005)
10.1016/S1574-1400(05)01007-8
Chapter 7 Empirical Force Fields for Proteins: Current Status and Future Directions
Alexander D. MacKerell (2005)
10.1002/prot.21454
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases
M. Martí (2007)
10.1063/1.479049
A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
M. Eichinger (1999)
10.1007/BF00402823
The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations
U. Ryde (1996)
10.1021/JA0654074
Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study.
David Rinaldo (2007)
10.1021/J100028A030
Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential
David S. Hartsough (1995)
Phys
G. E. Crooks (1487)
10.1021/IC0521168
Catalytic mechanism of dopamine β-monooxygenase mediated by Cu(III)-oxo
K. Yoshizawa (2006)
10.1126/SCIENCE.1411573
A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.
J. Gao (1992)
10.1021/JP0670743
Stabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfers.
Q. Xu (2007)
10.1063/1.1523915
Development of a simple, self-consistent polarizable model for liquid water
Haibo Yu (2003)
10.1021/JA062082I
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II.
M. Hoffmann (2006)
10.1021/ct050318n
Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution.
H. Gunaydin (2007)
10.1016/J.SBI.2007.03.015
Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II.
E. Sproviero (2007)
10.1021/JA026279W
The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations.
J. Schöneboom (2002)
10.1146/ANNUREV.PHYSCHEM.53.082301.113146
Transition path sampling: throwing ropes over rough mountain passes, in the dark.
P. Bolhuis (2002)
10.1021/JP0356158
pKa calculations with QM/MM free energy perturbations
Guohui Li (2003)
Chem
D. M. Philipp (1494)
10.1021/JP0656882
Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases.
N. Díaz (2006)
10.1021/JP072373T
A QM/MM study of the Bergman reaction of dynemicin A in the minor groove of DNA.
T. Tuttle (2007)
10.1039/A801266K
Sampling ensembles of deterministic transition pathways
P. Bolhuis (1998)
10.1021/AR050027T
Computational studies of the primary phototransduction event in visual rhodopsin.
J. Gascón (2006)
10.1016/J.THEOCHEM.2003.08.088
Computer modelling of enzyme reactions
G. Náray-Szabó (2003)
10.1021/JP056626Z
Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study.
Arturo Robertazzi (2006)
10.1021/ct600346p
Exploiting QM/MM Capabilities in Geometry Optimization:  A Microiterative Approach Using Electrostatic Embedding.
J. Kästner (2007)
10.1021/JP070699W
pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications.
D. Riccardi (2007)
10.1021/JA0600882
Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein.
C. Corminboeuf (2006)
10.1016/S0010-4655(02)00374-0
Determining the density of states for classical statistical models by a flat-histogram random walk☆
D. P. Landau (2002)
10.1016/J.THEOCHEM.2003.08.010
Geometry optimization methods for modeling large molecules
Ö. Farkas (2003)
Theory Comput
H. Gunaydin (1035)
10.1021/JA069176C
Ultrafast deactivation of an excited cytosine-guanine base pair in DNA.
G. Groenhof (2007)
10.1063/1.1860560
Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods.
G. Cisneros (2005)
10.1016/0022-2836(76)90311-9
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
A. Warshel (1976)
10.1002/prot.21482
Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl‐CoA enolization in citrate synthase
Marc W. van der Kamp (2007)
10.1016/J.THEOCHEM.2006.06.008
Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase
Pär Söderhjelm (2006)
10.1016/j.cpc.2005.01.022
Accounting for polarization in molecular simulation
Haibo Yu (2005)
10.1021/JP0496405
A variational definition of electrostatic potential derived charges
A. Laio (2004)
10.1063/1.1477182
Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules
G. A. DiLabio (2002)
10.1016/J.JSB.2005.11.014
Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis: a hybrid QM/MM study.
Xue-Feng Gao (2006)
10.1021/JP071878G
Protein environment facilitates O2 binding in non-heme iron enzyme. An insight from ONIOM calculations on isopenicillin N synthase (IPNS).
Marcus Lundberg (2007)
10.1021/CT700167B
The Design of a Next Generation Force Field: The X-POL Potential.
W. Xie (2007)
10.1529/BIOPHYSJ.107.108464
Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes.
Nadtanet Nunthaboot (2007)
10.1021/BK-1998-0712.CH004
On the Treatment of Link Atoms in Hybrid Methods
I. Antes (1998)
10.1016/J.CBPA.2007.01.684
QM/MM studies of enzymes.
H. Senn (2007)
10.1039/b713197f
QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.
Daan P. Geerke (2008)
10.1063/1.1520134
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
D. Das (2002)
10.1063/1.1834899
Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods.
Y. Zhang (2005)
10.1021/JA0452830
Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase.
Alejandro Crespo (2005)
10.1021/JA021424R
Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.
C. Guimarães (2003)
10.1098/rsta.2004.1529
Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts
C. R. Catlow (2005)
10.1063/1.2424700
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.
H. Li (2007)
Chem
J. Wang (1074)
10.1002/BIP.20642
Computational study of the absorption spectra of green fluorescent protein mutants.
S. Patnaik (2007)
10.1021/JA062272T
Transition State Stabilization and α-Amino Carbon Acidity in Alanine Racemase
D. Major (2006)
10.1186/1752-153X-1-19
Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions
A. Mulholland (2007)
10.1039/B604263P
Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations.
K. Spiegel (2006)
10.1021/JP034286G
Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations
Guohui Li (2003)
10.1002/ADSC.200303146
Biocatalytic Potential of p-Hydroxybenzoate Hydroxylase from Rhodococcus rhodnii 135 and Rhodococcus opacus 557
A. Jadan (2004)
10.1021/J100148A005
Calculation of solvation free energies using a density functional/molecular dynamics coupled potential
R. Stanton (1993)
10.1002/(SICI)1096-987X(199703)18:4<463::AID-JCC2>3.0.CO;2-R
Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs
U. Eichler (1997)
10.1080/00268970500417846
Geometry optimization with QM/MM methods II: Explicit quadratic coupling
T. Vreven (2006)
10.1021/JP066852O
Mechanism of nitrite reduction at T2Cu centers: electronic structure calculations of catalysis by copper nitrite reductase and by synthetic model compounds.
M. Sundararajan (2007)
10.1021/JA071533B
DNA Polymerase β Catalysis: Are Different Mechanisms Possible?
I. Alberts (2007)
10.1021/BI700515Q
A quantum mechanics/molecular mechanics study of the catalytic mechanism and product specificity of viral histone lysine methyltransferase.
X. Zhang (2007)
10.1063/1.472045
An effective fragment method for modeling solvent effects in quantum mechanical calculations
P. Day (1996)
10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
J. Wang (2000)
10.1021/JA039557F
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
G. Groenhof (2004)
10.1016/S0166-1280(03)00296-3
Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding
A. Fornili (2003)
10.1021/JP0634858
Understanding the enzymatic activity of 4-oxalocrotonate tautomerase and its mutant analogues: a computational study.
T. Tuttle (2006)
10.1021/JP0543328
Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase.
G. Cisneros (2006)
10.1021/JP951762X
Application of the New “Integrated MO + MM” (IMOMM) Method to the Organometallic Reaction Pt(PR3)2 + H2 (R = H, Me, t-Bu, and Ph)
Toshiaki Matsubara (1996)
10.1007/3-540-35284-8_17
Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods
U. Rothlisberger (2006)
10.1063/1.1765651
Mapping potential energy surfaces.
Yudong Wu (2004)
10.1063/1.2403847
Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment.
M. Valiev (2006)
10.1021/JP962071J
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
Mats Svensson (1996)
10.1002/jcc.10093
Quantum chemical geometry optimizations in proteins using crystallographic raw data
U. Ryde (2002)
10.1103/PHYSREVLETT.99.058104
Solvent effects on charge spatial extent in DNA and implications for transfer.
Yves A. Mantz (2007)
10.1016/J.JMGM.2007.04.009
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.
Suwipa Saen-oon (2007)
10.1016/S1359-6446(05)03611-1
Modelling enzyme reaction mechanisms, specificity and catalysis.
A. Mulholland (2005)
10.1021/BK-1994-0569.CH009
Effective Fragment Method for Modeling Intermolecular Hydrogen-Bonding Effects on Quantum Mechanical Calculations
Jan H. Jenson (1994)
10.1021/JP066478S
Why urea eliminates ammonia rather than hydrolyzes in aqueous solution.
A. Alexandrova (2007)
10.1021/JP045571I
A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.
B. Ensing (2005)
10.1016/S0166-1280(98)00391-1
CHEMICAL REACTIVITY STUDIED BY HYBRID QM/MM METHODS
I. H. Hillier (1999)
10.1021/JP055412E
The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: a QM/MM study.
E. Derat (2006)
10.1016/S1367-5931(02)00016-9
Combined quantum and molecular mechanics calculations on metalloproteins.
U. Ryde (2003)
10.1016/S0065-3233(03)66002-X
Force fields for protein simulations.
J. Ponder (2003)
10.1021/JP960690M
QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone
M. Thompson (1996)
10.1016/S0166-1280(96)80005-4
Tetrahedral intermediate formation in the acylation step of acetylcholinesterases. A combined quantum chemical and molecular mechanical model
V. V. Vasilyev (1994)
10.1002/CPHC.200400602
Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.
J. Pu (2005)
10.1002/(SICI)1096-987X(19991115)20:14<1468::AID-JCC2>3.0.CO;2-0
Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
D. Philipp (1999)
10.1080/00268970310001593286
Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase
K. E. Ranaghan (2003)
10.1016/S0166-1280(03)00286-0
An approximate DFT method for QM/MM simulations of biological structures and processes
M. Elstner (2003)
10.1002/QUA.20910
Modeling dioxygen binding to the non‐heme iron‐containing enzymes
A. Nemukhin (2006)
10.1021/ct6000686
Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases.
K. Bravaya (2006)
Chem
P. Cieplak (1057)
10.1021/JA066150C
Proton shuttles and phosphatase activity in soluble epoxide hydrolase.
M. De Vivo (2007)
10.1002/ANIE.200602711
High-accuracy computation of reaction barriers in enzymes.
F. Claeyssens (2006)
Computer Simulation in Condensed Matter: From Materials to Chemical Biology. Vol. 2
M. Ferrario (2006)
10.1021/ct058001a
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)].
S. Martí (2006)
10.1021/ct049930p
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.
V. Anisimov (2005)
10.1063/1.476378
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
C. Dellago (1998)
10.1021/JP053182Y
Polarizable empirical force field for alkanes based on the classical Drude oscillator model.
I. Vorobyov (2005)
10.1021/JA067899Q
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.
S. Sinnecker (2007)
10.1021/JA049376T
Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.
Borys Szefczyk (2004)
10.1021/JP049633G
Hybrid QM/MM Potentials of Mean Force with Interpolated Corrections
J. Ruiz-Pernía (2004)
10.1039/A909486E
Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
S. Billeter (2000)
10.1021/JP973480Y
Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin
Jörg Bentzien (1998)
10.1016/J.BMC.2007.03.027
Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.
C. Alves (2007)
10.1021/ct050202r
The IMOMM (Integrated Molecular Orbitals/Molecular Mechanics) Approach for Ligand-Stabilized Metal Clusters. Comparison to Full Density Functional Calculations for the Model Thiolate Cluster Cu13(SCH2CH3)8.
A. Genest (2006)
Mulholland in Quantum Medicinal Chemistry (Methods Princ
F. Perruccio (2003)
10.1039/9781847555373
Modelling molecular structure and reactivity in biological systems
Computational Chemists (2006)
10.1016/J.BPC.2006.04.008
Polarization effects and charge transfer in the KcsA potassium channel.
D. Bucher (2006)
10.1063/1.1336570
Generalized solvent boundary potential for computer simulations
W. Im (2001)
10.1111/J.1432-1033.1992.TB16950.X
Frontier orbital study on the 4-hydroxybenzoate-3-hydroxylase-dependent activity with benzoate derivatives.
J. Vervoort (1992)
10.1021/BI061737P
The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As.
Q. Xu (2007)
Theory Comput
K. Bravaya (1175)
10.1021/ct049941i
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.
K. Nam (2005)
10.1021/JP0469968
Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations.
Brent A. Gregersen (2005)
10.1021/JP984498R
Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Initio Quantum Chemistry
H. Stern (1999)
10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
Alexander D. MacKerell (2000)
10.1021/JP0459108
Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes.
Ahmet Altun (2005)
10.1039/B313759G
Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.
K. E. Ranaghan (2004)
10.1021/JA0369156
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 (2004)
Chem
P. Ren (1506)
10.1021/JP011048H
Energetics and Dynamics of Enzymatic Reactions
Jordi Villà and (2001)
Chem
U. Ryde (1070)
10.1021/JA00124A002
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell (1995)
10.1103/PhysRevLett.92.170601
Reconstructing the density of states by history-dependent metadynamics.
C. Micheletti (2004)
10.1021/J100016A067
Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide
J. Caldwell (1995)
10.1021/JP057342H
Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach.
Anan Tongraar (2006)
10.1016/S0166-1280(03)00285-9
QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis
P. Sherwood (2003)
10.1103/PhysRevE.60.2721
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences.
G. Crooks (1999)
10.1021/JA0520924
Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling.
Christine M. Bathelt (2005)
Organometallic Bonding and Reactivity: Fundamental Studies
J. Brown (1999)
10.1063/1.1330207
Low-order scaling local electron correlation methods. IV. Linear scaling local coupled-cluster (LCCSD)
M. Schütz (2001)
10.1096/fasebj.9.7.7737455
Structure and mechanism of para‐hydroxybenzoate hydroxylase
B. Entsch (1995)
10.1016/J.JINORGBIO.2004.06.006
Protonation status of metal-bound ligands can be determined by quantum refinement.
K. Nilsson (2004)
10.1529/BIOPHYSJ.105.078097
The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure.
N. Strickland (2006)
10.1007/S002140050217
Solvent effects on the nπ* transition of pyrimidine in aqueous solution
J. Gao (1997)
10.1002/1096-987X(200012)21:16<1470::AID-JCC5>3.0.CO;2-L
Combining quantum mechanics and interatomic potential functions in ab initio studies of extended systems
Joachim Sauer (2000)
10.1016/S0920-5861(98)00483-0
Towards more realistic computational modeling of homogenous catalysis by density functional theory: combined QM/MM and ab initio molecular dynamics
T. Woo (1999)
10.1002/jcc.20398
Systematic QM/MM investigation of factors that affect the cytochrome P450‐catalyzed hydrogen abstraction of camphor
Ahmet Altun (2006)
10.1021/JP063520A
Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes.
J. J. Ruiz-Pernía (2006)
10.1021/CR00023A010
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
J. Åqvist (1993)
10.1073/pnas.0702188104
Coupling of hydrogenic tunneling to active-site motion in the hydrogen radical transfer catalyzed by a coenzyme B12-dependent mutase
A. Dybala-Defratyka (2007)
10.1002/jcc.10355
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Sandeep Patel (2004)
10.1021/JA0676861
The effect of a water molecule on the mechanism of formation of compound 0 in horseradish peroxidase.
E. Derat (2007)
10.1021/ct0500850
QM/MM Study of the NMR Spectroscopy of the Retinyl Chromophore in Visual Rhodopsin.
J. Gascón (2005)
10.1021/JP0548265
Duocarmycins binding to DNA investigated by molecular simulation.
K. Spiegel (2006)
Medicinal Chemistry for Drug Discovery (Eds.
J.-L. Rivail (2004)
10.1021/JP0673617
Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.
A. Heyden (2007)
10.1146/ANNUREV.PHYSCHEM.53.091301.150114
Quantum mechanical methods for enzyme kinetics.
J. Gao (2002)
10.1080/08927020211977
An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles
Lula Rosso (2002)
Chem
T. Ishida (1463)
10.1002/jcc.540160911
IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states
F. Maseras (1995)
10.1021/BI0515624
Origin and consequences of steric strain in the rhodopsin binding pocket.
Minoru Sugihara (2006)
10.1063/1.2823055
Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase.
R. Mata (2008)
10.1529/BIOPHYSJ.104.041590
The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.
K. Nilsson (2004)
10.1103/PHYSREVB.58.7260
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
M. Elstner (1998)
10.1023/A:1023208217925
Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems
G. Crooks (1998)
QM/MM Methods Angewandte Chemie
L. Pauling (2009)
10.1529/BIOPHYSJ.106.102509
The protonation state of the Glu-71/Asp-80 residues in the KcsA potassium channel: a first-principles QM/MM molecular dynamics study.
D. Bucher (2007)
10.1021/JP0493632
QM/MM Study of the Product−Enzyme Complex in P450cam Catalysis
H. Lin (2004)
10.1007/128_2006_084
QM/MM Methods for Biological Systems
H. Senn (2006)
10.1021/jp973084f
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell (1998)
10.1007/S00214-006-0143-Z
QM/MM: what have we learned, where are we, and where do we go from here?
H. Lin (2006)
10.1021/OM050840S
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)
Sheng-Yong Yang (2006)
10.1021/JA972723X
Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution
R. Stanton (1998)
10.1021/JP067307Q
YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.
Y. Shao (2007)
10.1073/pnas.102649299
Energetics of glycerol conduction through aquaglyceroporin GlpF
M. Jensen (2002)
10.1021/BI061953Y
A quantum mechanics/molecular mechanics study of the catalytic mechanism of the thymidylate synthase.
Natalia Kanaan (2007)
10.1021/JP044387U
Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM strategy.
S. Martí (2005)
10.1021/JP0520953
Activation free energy of catechol O-methyltransferase. Corrections to the potential of mean force.
M. Roca (2006)
10.1073/pnas.0732000100
Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450
V. Guallar (2003)
10.1002/9780470125847.CH3
Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials
Jiali Gao (2007)
Chem
G. A. Kaminski (1531)
10.1016/S0959-440X(98)80048-1
Quantum mechanical calculations on biological systems.
R. Friesner (1998)
10.1021/JP9809890
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
J. Gao (1998)
10.1021/JP021625H
Ab Initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution
M. Štrajbl (2002)
10.1016/0022-2836(89)90093-4
Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.
C. Brooks (1989)
10.1146/ANNUREV.BIOPHYS.32.110601.141807
Computer simulations of enzyme catalysis: methods, progress, and insights.
A. Warshel (2003)
kyl in Quantum Medicinal Chemistry (Methods Princ
M. Per (2003)
10.1021/JA062876X
The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation.
Alejandro Crespo (2006)
10.1021/JP003919D
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides†
George A. Kaminski and (2001)



This paper is referenced by
10.1002/jcc.23208
A numerically stable restrained electrostatic potential charge fitting method
J. Zeng (2013)
10.1016/J.CPLETT.2010.03.089
Optimal control design of laser pulses for mode specific vibrational excitation in an enzyme–substrate complex
Qinghua Ren (2010)
10.1088/0953-8984/22/41/413101
Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.
Yohsuke Hagiwara (2010)
10.1016/B978-0-12-386485-7.00001-6
Application of computational methods to the design of fatty acid amide hydrolase (FAAH) inhibitors based on a carbamic template structure.
A. Lodola (2011)
10.1515/psr-2017-0178
Description of excited states in photochemistry with theoretical methods
Thomas Merz (2018)
Quantum-mechanical studies of reactions performed by cytochrome P 450 enzymes
P. Rydberg (2013)
10.1002/minf.201300131
Integrating Computational Modeling and Experimental Assay to Discover New Potent ACE‐Inhibitory Peptides
Yanrong Ren (2014)
10.1002/jcc.21615
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation
S. Re (2011)
10.1021/bi500060h
Quantum mechanics/molecular mechanics studies of the mechanism of falcipain-2 inhibition by the epoxysuccinate E64.
K. Arafet (2014)
Protein Flexibility: From local to global motions. A computational study
M. S. Martínez (2014)
10.1002/QUA.22600
Entropy–energy balance in base catalyzed keto-enol interconversion: A joint theoretical and experimental investigation†
M. Aschi (2011)
10.1016/J.COMPTC.2014.05.013
The development and validation of a pseudoatoms approach for combined quantum mechanics and molecular mechanics calculations of polypeptide
Z. Zhang (2014)
10.1002/prot.24506
Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B
P. Schopf (2014)
10.1002/jcc.23225
QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface
T. Kerber (2013)
10.1021/jp4020146
Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.
N. Plotnikov (2013)
10.1016/j.bbapap.2011.08.014
QM/MM study of the mechanism of enzymatic limonene 1,2-epoxide hydrolysis.
Q. Hou (2012)
10.1063/1.4811292
Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations.
Magnus Schwörer (2013)
10.1007/s00894-016-3004-2
QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme
Xia Mu (2016)
10.1021/jp5088702
Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases
M. Khrenova (2014)
10.1021/ct3002514
Origin of Fluorescence in 11-cis Locked Bovine Rhodopsin.
Elena N. Laricheva (2012)
10.3390/molecules23112830
Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF4]
E. A. Vázquez-Montelongo (2018)
10.1073/pnas.1319854110
Quantitative exploration of the molecular origin of the activation of GTPase
Ram Prasad B (2013)
10.1002/anie.201309174
Solving chemical problems with a mixture of quantum-mechanical and molecular mechanics calculations: Nobel Prize in Chemistry 2013.
G. Groenhof (2013)
10.1007/978-3-319-43030-0_9
Multiscale Modelling of Molecular Processes for Biomedical and Nanotechnology Applications with MBN Explorer
A. Solov'Yov (2017)
Calculating molecular properties in realistic environments
M. T. P. Beerepoot (2016)
10.1021/ct400953f
Multisurface Adiabatic Reactive Molecular Dynamics.
T. Nagy (2014)
10.1021/acs.chemrev.6b00163
Coarse-Grained Protein Models and Their Applications.
S. Kmiecik (2016)
10.3389/fmicb.2015.00660
Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa
J. Dreier (2015)
10.1021/acs.jcim.8b00605
Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package
A. Marion (2019)
"Subsystem quantum mechanics can … yield speed, predictivity and insight in resolving problems of biochemistry, medicinal chemistry and their applications in drug design."
C. F. Matta (2011)
10.1016/bs.apcsb.2018.07.001
Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms.
Jon Ainsley (2018)
10.3389/fchem.2017.00076
The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study
M. Hitzenberger (2017)
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