Citation Impact
Citing Papers
On the relationship between folding and chemical landscapes in enzyme catalysis
2008 StandoutNobel
AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS
2005
High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
2007 StandoutScienceNobel
GPCR Engineering Yields High-Resolution Structural Insights into β 2 -Adrenergic Receptor Function
2007 StandoutScienceNobel
Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O 2 activation
2019 StandoutNobel
The 2.6 Angstrom Crystal Structure of a Human A 2A Adenosine Receptor Bound to an Antagonist
2008 StandoutScience
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Structure⧸Function Correlations of Proteins using MM, QM⧸MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress
2003 StandoutNobel
The amide bond: pitfalls and drawbacks of the link atom scheme
2003
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
2003
Strong and Reversible Binding of Carbon Dioxide in a Green Metal–Organic Framework
2011 StandoutNobel
QM/MM Methods for Biomolecular Systems
2009 Standout
Dioxygen affinity in heme proteins investigated by computer simulation
2006
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method
2002
Cofactor-independent oxidases and oxygenases
2010
Crystal structure of the human β2 adrenergic G-protein-coupled receptor
2007 StandoutNatureNobel
Computational Enzyme Design
2013 StandoutNobel
Some critical issues in the application of quantum mechanics/molecular mechanics methods to the study of transition metal complexes
2003
Protonation status of metal-bound ligands can be determined by quantum refinement
2004
Design of Protein–Ligand Binding Based on the Molecular-Mechanics Energy Model
2008
The Protonation Status of Compound II in Myoglobin, Studied by a Combination of Experimental Data and Quantum Chemical Calculations: Quantum Refinement
2004
The Amber biomolecular simulation programs
2005 Standout
The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions
2009 StandoutNobel
Combined quantum and molecular mechanics calculations on metalloproteins
2003
The structure and function of G-protein-coupled receptors
2009 StandoutNatureNobel
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods
2003
NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
2005
The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2 Å Crystal Structure
2004
Structure of a β1-adrenergic G-protein-coupled receptor
2008 StandoutNatureNobel
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens
2003
Simulating enzyme reactions: Challenges and perspectives
2001
Generalized Hybrid‐Orbital Method for Combining Density Functional Theory with Molecular Mechanicals
2005
The Importance of the Active Site Histidine for the Activity of Epoxide‐ or Aziridine‐Based Inhibitors of Cysteine Proteases
2006
Computational enzymology
2000
Geometry optimization and transition state search in enzymes: Different options in the microiterative method
2004
Copper(I)-Catalyzed Synthesis of Azoles. DFT Study Predicts Unprecedented Reactivity and Intermediates
2004 StandoutNobel
Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
2000
CO2 Absorption in Aqueous Solutions of Alkanolamines: Mechanistic Insight from Quantum Chemical Calculations
2007
Quantitative exploration of the molecular origin of the activation of GTPase
2013 StandoutNobel
Ab Initio Evaluation of the Potential Surface for General Base- Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases
2000 StandoutNobel
A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase
2003
Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution
2008 StandoutNobel
Combined QM/MM Study of the Mechanism and Kinetic Isotope Effect of the Nucleophilic Substitution Reaction in Haloalkane Dehalogenase
2003
Continuum solvation models: Dissecting the free energy of solvation
2003
Improving Protein Expression, Stability, and Function with ProteinMPNN
2024 StandoutNobel
Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis
2006 StandoutNobel
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome
2011 StandoutNobel
Antibiotic Deactivation by a Dizinc β-Lactamase: Mechanistic Insights from QM/MM and DFT Studies
2007
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
1999
Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism
2004
Ab Initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution
2002 StandoutNobel
Ab initiomolecular dynamics: basic concepts, current trends and novel applications
2002
The ONIOM Method and Its Applications
2015
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
2000
Geometry optimization methods for modeling large molecules
2003
On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach
2007
Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The SN2 Reaction of Dehalogenase as a General Benchmark
2004 StandoutNobel
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
2000
On the Mechanism of Hydrolysis of Phosphate Monoesters Dianions in Solutions and Proteins
2006 StandoutNobel
Mechanisms of Tetrazole Formation by Addition of Azide to Nitriles
2002 StandoutNobel
Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method
2004
Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations
2005
A new paradigm for electrostatic catalysis of radical reactions in vitamin B 12 enzymes
2007 StandoutNobel
Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods
1999
New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
2007
Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase
2018 StandoutNobel
Theoretical study of structure of catalytic copper site in nitrite reductase
2004
Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order “chain-of-replicas” methods
2005
Quantum refinement—a combination of quantum chemistry and protein crystallography
2003
Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization
2003 StandoutNobel
The IMOMM method opens the way for the accurate calculation of “real” transition metal complexes
2000
A QM/MM Study of the Racemization of Vinylglycolate Catalyzed by Mandelate Racemase Enzyme
2001
All Electron Quantum Chemical Calculation of the Entire Enzyme System Confirms a Collective Catalytic Device in the Chorismate Mutase Reaction
2005
Inhibitor Binding by Metallo-β-lactamase IMP-1 from Pseudomonas aeruginosa: Quantum Mechanical/Molecular Mechanical Simulations
2007
Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase
2003 StandoutNobel
An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides
2010 StandoutScience
Macrophomate Synthase: QM/MM Simulations Address the Diels−Alder versus Michael−Aldol Reaction Mechanism
2005
ASEP/MD: A program for the calculation of solvent effects combining QM/MM methods and the mean field approximation
2003
The sequential Monte Carlo-quantum mechanics methodology. Application to the solvent effects in the Stokes shift of acetone in water
2003
Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin
1998 StandoutNobel
Computational Insights into the Mechanism of Radical Generation in B12-Dependent Methylmalonyl-CoA Mutase
2006
Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems
2008
Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
2013 StandoutNobel
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
2005
A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
2002
Why Is Tetrazole Formation by Addition of Azide to Organic Nitriles Catalyzed by Zinc(II) Salts?
2003 StandoutNobel
Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations
2007
An empirical valence bond model for proton transfer in water
1998
Effects of Point Mutation on Enzymatic Activity: Correlation between Protein Electronic Structure and Motion in Chorismate Mutase Reaction
2010
Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches
2000
Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method
1996
The nature of the hydrated excess proton in water
1999 StandoutNature
Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: A design-carbon atom with five valence electrons
2007
YinYang Atom: A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model
2007
QUANTUM MECHANICAL METHODS FOR ENZYME KINETICS
2002
Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations
2006
Variational optimization of effective atom centered potentials for molecular properties
2004
Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method
2000
Simple minimum principle to derive a quantum-mechanical/ molecular-mechanical method
2004
Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies
2008 StandoutNobel
Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems
2005
AB INITIO MOLECULAR DYNAMICS WITH DENSITY FUNCTIONAL THEORY
2002
1998
QM/MM Boundaries Across Covalent Bonds: A Frozen Localized Molecular Orbital-Based Approach for the Effective Fragment Potential Method
2000
On Possible Pitfalls in ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions
2005 StandoutNobel
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
2005
Peptide Hydrolysis in Thermolysin: Ab Initio QM/MM Investigation of the Glu143-Assisted Water Addition Mechanism
2007
Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination
2008 StandoutNobel
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
1998
Toward Identification of the Compound I Reactive Intermediate in Cytochrome P450 Chemistry: A QM/MM Study of Its EPR and Mössbauer Parameters
2005
Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The Reaction Free Energy Profiles of the Acylation Process
2003
A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region
1999
Geometry optimization with QM/MM methods II: Explicit quadratic coupling
2006
Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution
1998 StandoutNobel
Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights
2003 StandoutNobel
Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions
2006 StandoutNobel
QM/MM: what have we learned, where are we, and where do we go from here?
2006
Computer Simulation Studies of the Catalytic Mechanism of Human Aldose Reductase
2000 StandoutNobel
Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase
2003 StandoutNobel
The effect of ligand efficacy on the formation and stability of a GPCR-G protein complex
2009 StandoutNobel
Quantum Mechanical Continuum Solvation Models
2005 Standout
Antibiotic Binding to Dizinc β-Lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies
2007
Theoretical Insight into Gate-Opening Adsorption Mechanism and Sigmoidal Adsorption Isotherm into Porous Coordination Polymer
2018 StandoutNobel
Mechanism of Triphosphate Hydrolysis in Aqueous Solution: QM/MM Simulations in Water Clusters
2006
How important are entropic contributions to enzyme catalysis?
2000 StandoutNobel
Mechanisms and Free Energies of Enzymatic Reactions
2006
Computational Approaches: Reaction Trajectories, Structures, and Atomic Motions. Enzyme Reactions and Proficiency
2006
Combining quantum mechanics and interatomic potential functions inab initio studies of extended systems
2000
Methods for optimizing large molecules. Part III. An improved algorithm for geometry optimization using direct inversion in the iterative subspace (GDIIS)
2002
Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems
2006 StandoutNobel
Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne
2016 StandoutNobel
Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations
2007
Generalized solvent boundary potential for computer simulations
2001
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics
2004
Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin
2003 StandoutNobel
Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods
2004
Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution
1998
Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
2000
Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein
2006
A Hybrid Potential Reaction Path and Free Energy Study of the Chorismate Mutase Reaction
2001
Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition
2017 StandoutNobel
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
2010 StandoutNobel
Works of Gérald Monard being referenced
An efficient method for the coordinate transformation problem of massively three-dimensional networks
2001
Linear scaling algorithm for the coordinate transformation problem of molecular geometry optimization
2000
The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface
2002
Deamidation of Asparagine Residues: Direct Hydrolysis versus Succinimide-Mediated Deamidation Mechanisms
2009
Modeling of Peptide Hydrolysis by Thermolysin. A Semiempirical and QM/MM Study
1998
Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems
1999
Determination of enzymatic reaction pathways using QM/MM methods
2003
Reaction Mechanism of Deamidation of Asparaginyl Residues in Peptides: Effect of Solvent Molecules
2006
Insights in the Peptide Hydrolysis Mechanism by Thermolysin: A Theoretical QM/MM study
2000
Oxygen Pressurized X-Ray Crystallography: Probing the Dioxygen Binding Site in Cofactorless Urate Oxidase and Implications for Its Catalytic Mechanism
2008
Hybrid classical quantum force field for modeling very large molecules
1996