Related references
Note: Only part of the references are listed.Integrating steepest-descent reaction pathways for large molecules
Hrant P. Hratchian et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
Tsutomu Kawatsu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
On the Convergence of QM/MM Energies
LiHong Hu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Photochemistry of Visual Pigment in a G(q) Protein-Coupled Receptor (GPCR)-Insights from Structural and Spectral Tuning Studies on Squid Rhodopsin
Sivakumar Sekharan et al.
CHEMISTRY-A EUROPEAN JOURNAL (2010)
Link atom bond length effect in ONIOM excited state calculations
Marco Caricato et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics
Marcus Lundberg et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Charge Transfer Across ONIOM OM/QM Boundaries: The Impact of Model System Preparation
Nicholas J. Mayhall et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Geometry Optimization with Multilayer Methods Using Least-Squares Minimization
Wenkel Liang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Benchmark of Electronically Excited States for Semiempirical Methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2
Mario R. Silva-Junior et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm
Bo Wang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Real size of ligands, reactants and catalysts: Studies of structure, reactivity and selectivity by ONIOM and other hybrid computational approaches
Valentine P. Ananikov et al.
JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL (2010)
Competitive Mechanistic Pathways for Green-to-Red Photoconversion in the Fluorescent Protein Kaede: A Computational Study
Xin Li et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman
Xin Li et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
What is the Real Nature of Ferrous Soybean Lipoxygenase-1? A New Two-Conformation Model Based on Combined ONIOM(DFT:MM) and Multireference Configuration Interaction Characterization
Hajime Hirao et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2010)
Primary Events of Photodynamics in Reversible Photoswitching Fluorescent Protein Dronpa
Xin Li et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2010)
ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants
Lung Wa Chung et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Conical intersection dynamics of the primary photoisomerization event in vision
Dario Polli et al.
NATURE (2010)
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
Justin B. Siegel et al.
SCIENCE (2010)
QM/MM Methods for Biomolecular Systems
Hans Martin Senn et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2009)
Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4-Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue
Peng Tao et al.
BIOCHEMISTRY (2009)
Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation
Shigehiko Hayashi et al.
BIOPHYSICAL JOURNAL (2009)
myo-Inositol oxygenase: a radical new pathway for O2 and C-H activation at a nonheme diiron cluster
J. Martin Bollinger et al.
DALTON TRANSACTIONS (2009)
Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method
Guishan Zheng et al.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2009)
Approximated electron repulsion integrals: Cholesky decomposition versus resolution of the identity methods
Florian Weigend et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods
Satoshi Maeda et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Toward a Practical Method for Adaptive QM/MM Simulations
Rosa E. Bulo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes
Hao Hu et al.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (2009)
DFT and ONIOM(DFT:MM) Studies on Co-C Bond Cleavage and Hydrogen Transfer in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism?
Xin Li et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Insights into the (Superoxo)Fe(III)Fe(III) Intermediate and Reaction Mechanism of myo-Inositol Oxygenase: DFT and ONIOM(DFT:MM) Study
Hajime Hirao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Reassessment of the Reaction Mechanism in the Heme Dioxygenases
Nishma Chauhan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Evidence for a ferryl intermediate in a heme-based dioxygenase
Ariel Lewis-Ballester et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
Hao Hu et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2008)
Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques:: Implementation blending ONIOM and empirical valence bond theory
Isaiah Sumner et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
QM:QM electronic embedding using Mulliken atomic charges:: Energies and analytic gradients in an ONIOM framework
Hrant P. Hratchian et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Quantum chemistry on graphical processing units.: 1.: Strategies for two-electron integral evaluation
Ivan S. Ufimtsev et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Searching for conical intersections of potential energy surfaces with the ONIOM method: Application to previtamin D
Michael J. Bearpark et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2008)
Mechanism of Spectral Tuning Going from Retinal in Vacuo to Bovine Rhodopsin and its Mutants: Multireference ab Initio Quantum Mechanics/Molecular Mechanics Studies
Ahmet Altun et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II
Marius Wanko et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Density functional theory study on a missing piece in understanding of heme chemistry: The reaction mechanism for indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase
Lung Wa Chung et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Light-dependent regulation of structural flexibility in a photochromic fluorescent protein
Hideaki Mizuno et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Chromophore protonation state controls photoswitching of the fluoroprotein asFP595
Lars V. Schaefer et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Advances in fluorescent protein technology
Nathan C. Shaner et al.
JOURNAL OF CELL SCIENCE (2007)
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
James J. P. Stewart
JOURNAL OF MOLECULAR MODELING (2007)
Structural basis for reversible photoswitching in Dronpa
Martin Andresen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations
Yan Zhang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Parameter calibration of transition-metal elements for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method: Sc, Ti, Fe, Co, and Ni
Guishan Zheng et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Combined QM/MM molecular dynamics study on a condensed-phase SN2 reaction at nitrogen:: The effect of explicitly including solvent polarization
Daan P. Geerke et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes
Pankaz K. Sharma et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The ONIOM molecular dynamics method for biochemical applications: Cytidine deaminase
Toshiaki Matsubara et al.
CHEMICAL PHYSICS LETTERS (2007)
QM/MM: what have we learned, where are we, and where do we go from here?
Hai Lin et al.
THEORETICAL CHEMISTRY ACCOUNTS (2007)
Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase
Farhad Forouhar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Does Cob(II)alamin act as a conductor in coenzyme B-12 dependent mutases?
Pawel M. Kozlowski et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2007)
Modeling enzymatic reactions involving transition metals
Per E. M. Siegbahn et al.
ACCOUNTS OF CHEMICAL RESEARCH (2006)
Performance evaluation of the three-layer ONIOM method: Case study for a zwitterionic peptide
Keiji Morokuma et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Color tuning in rhodopsins:: The mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II
Michael Hoffmann et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
Thom Vreven et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Evidence for C-H cleavage by an iron-superoxide complex in the glycol cleavage reaction catalyzed by myo-inositol oxygenase
G Xing et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes
D Riccardi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Geometry optimization with QM/MM methods II: Explicit quadratic coupling
T Vreven et al.
MOLECULAR PHYSICS (2006)
Computational studies of the primary phototransduction event in visual rhodopsin
JA Gascón et al.
ACCOUNTS OF CHEMICAL RESEARCH (2006)
Crystal structure of human indoleamine 2,3-dioxygenase:: Catalytic mechanism of O2 incorporation by a heme-containing dioxygenase
H Sugimoto et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase
RA Kwiecien et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
A self-consistent space-domain decomposition method for QM/MM computations of protein electrostatic potentials
JA Gascon et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Improving the QM/MM description of chemical processes:: A dual level strategy to explore the potential energy surface in very large systems
S Martí et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
How the Co-C bond is cleaved in coenzyme B12 enzymes:: A theoretical study
KP Jensen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes
S Shaik et al.
CHEMICAL REVIEWS (2005)
Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations
H Lin et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2005)
Hybrid ab-initio/empirical molecular dynamics: Combining the ONIOM scheme with the atom-centered density matrix propagation (ADMP) approach
N Rega et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
How enzymes work: Analysis by modern rate theory and computer simulations
M Garcia-Viloca et al.
SCIENCE (2004)
Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting
R Ando et al.
SCIENCE (2004)
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems
BW Hopkins et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Radical carbon skeleton rearrangements:: Catalysis by coenzyme B12-dependent mutases
R Banerjee
CHEMICAL REVIEWS (2003)
Geometry optimization with QM/MM, ONIOM, and other combined methods.: I.: Microiterations and constraints
T Vreven et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Investigation of the S0→S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method
T Vreven et al.
THEORETICAL CHEMISTRY ACCOUNTS (2003)
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods
MP Repasky et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein
R Ando et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase
T Kerdcharoen et al.
CHEMICAL PHYSICS LETTERS (2002)
Effects of the protein environment on the structure and energetics of active sites of metalloenzymes.: ONIOM study of methane monooxygenase and ribonucleotide reductase
M Torrent et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution
T Vreven et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Structural and functional characterization of second-coordination sphere mutants of soybean lipoxpgenase-1
DR Tomchick et al.
BIOCHEMISTRY (2001)
New insight on the origin of the unusual acidity of Meldrum's acid from ab initio and combined QM/MM simulation study
Y Byun et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)
Proton transfer in bacteriorhodopsin: Structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method
S Hayashi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)
The ONIOM (our own N-layered integrated molecular orbital plus molecular mechanics) method for the first singlet excited (S1) state photoisomerization path of a retinal protonated Schiff base
T Vreven et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
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
YK Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
ONIOM as an efficient tool for calculating NMR chemical shielding constants in large molecules
PB Karadakov et al.
CHEMICAL PHYSICS LETTERS (2000)