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
An enumerative algorithm for de novo design of proteins with diverse pocket structures
2020 StandoutNobel
G protein-coupled receptors: In silico drug discovery in 3D
2004
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
2011 StandoutNobel
Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu 5 ) X-ray Structures
2018
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
Constraining the electron densities in DFT method as an effective way forab initio studies of metal-catalyzed reactions
2000 StandoutNobel
QM/MM Study of the Active Site of Free Papain and of the NMA-Papain Complex
1999
QM/MM Methods for Biomolecular Systems
2009 Standout
Modular click chemistry libraries for functional screens using a diazotizing reagent
2019 StandoutNatureNobel
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome
2013 StandoutNatureNobel
Modeling Biotransformation Reactions by Combined Quantum Mechanical / Molecular Mechanical Approaches: From Structure to Activity
2003
Utility of homology models in the drug discovery process
2004
Opportunities and challenges in phenotypic drug discovery: an industry perspective
2017
The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations
2006 StandoutNobel
Preorganization and Reorganization as Related Factors in Enzyme Catalysis: The Chorismate Mutase Case
2003
Drug delivery systems for RNA therapeutics
2022
Flexible effective fragment QM/MM method: Validation through the challenging tests
2003
Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction
2006 Standout
Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl‐CoA enolization in citrate synthase
2007
Dynamics of biochemical and biophysical reactions: insight from computer simulations
2001 StandoutNobel
Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations
2007
A new method to locate saddle points for reactions in solution by using the free‐energy gradient method and the mean field approximation
2004
The SWISS-MODEL Repository and associated resources
2008 Standout
Effect of the damping function in dispersion corrected density functional theory
2011 Standout
Simulating enzyme reactions: Challenges and perspectives
2001
On the Mechanism of ATP Hydrolysis in F1-ATPase
2003
Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex
2006
Generalized Hybrid‐Orbital Method for Combining Density Functional Theory with Molecular Mechanicals
2005
PREDICT modeling and in‐silico screening for G‐protein coupled receptors
2004
Computational enzymology
2000
Multiple roles of ATM in monitoring and maintaining DNA integrity
2010
Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase
2007
Lennard–Jones parameters for the combined QM/MM method using the B3LYP/6‐31G*/AMBER potential
2005
Ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Enzyme Catalysis: The Case of Histone Lysine Methyltransferase SET7/9
2007
Toward high-resolution prediction and design of transmembrane helical protein structures
2007 StandoutNobel
Copper(I)-Catalyzed Synthesis of Azoles. DFT Study Predicts Unprecedented Reactivity and Intermediates
2004 StandoutNobel
Combiningab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs
1997
Quantitative exploration of the molecular origin of the activation of GTPase
2013 StandoutNobel
Multicentered valence electron effective potentials: A solution to the link atom problem for ground and excited electronic states
2006
Reply to Karplus: Conformational dynamics have no role in the chemical step
2010 StandoutNobel
Frozen orbital QM/MM methods for density functional theory
2000
Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase
2003
A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
1999
Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis
2006 StandoutNobel
A Combined ONIOM Quantum Chemical−Molecular Dynamics Study of Zinc−Uracil Bond Breaking in Yeast Cytosine Deaminase
2006
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
2007 Standout
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome
2011 StandoutNobel
Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?
2002
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
1999
A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations
1997
Ground-State Structures and Vertical Excitations for the Kindling Fluorescent Protein asFP595
2006
Pillar[5]arene as a Co-Factor in Templating Rotaxane Formation
2013 StandoutNobel
OH + H2 → H2O + H. The importance of ‘exact exchange’ in density functional theory
1995
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
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization
2010 StandoutNobel
Mechanisms of Tetrazole Formation by Addition of Azide to Nitriles
2002 StandoutNobel
Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models
1998 Standout
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
A discrete solvent reaction field model for calculating molecular linear response properties in solution
2003
Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations
2004
Toward a general protocol for the study of static and dynamic properties of hydrogen-bonded systems
1997
Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
1996
Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization
2003 StandoutNobel
Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations
1999
Protein Pockets: Inventory, Shape, and Comparison
2010
Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase
2003 StandoutNobel
Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach
2004
Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments
2002
Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase
2011 StandoutNobel
A comparative study of two QM/MM methods testing the validity of the mean field approximation
2001
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
2005
Toward reliable density functional methods without adjustable parameters: The PBE0 model
1999 Standout
A theoretical study of solvent effects on the (n→π*)1 electron transition in acrolein
2004
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
2008 StandoutNobel
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
How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments?
2002 StandoutNobel
Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase
2004 StandoutNobel
A View at the Millennium: the Efficiency of Enzymatic Catalysis
2002
A consistent and accurateab initioparametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
2010 Standout
A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
2000
New strategies to incorporate the solvent polarization in self-consistent reaction field and free-energy perturbation simulations
1995
QUANTUM MECHANICAL METHODS FOR ENZYME KINETICS
2002
A discrete solvent reaction field model within density functional theory
2002
A mean field approach that combines quantum mechanics and molecular dynamics simulation: the water molecule in liquid water
1998
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
1998
Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model
1997
Cancer Genome Landscapes
2013 StandoutScience
High Oxidation State Multiple Metal−Carbon Bonds
2001 StandoutNobel
Ab initio/LD studies of chemical reactions in solution: Reference free-energy surfaces for acylation reactions occurring in serine and cysteine proteases
2000 StandoutNobel
Nonlinear optical response properties of molecules in condensed phases using the coupled cluster/dielectric continuum or molecular mechanics methods
2003
Electrostatic Basis for Enzyme Catalysis
2006 StandoutNobel
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase
2012 StandoutNobel
Solvent effects by means of averaged solvent electrostatic potentials: Coupled method
2000
Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases
2006
Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases
2001 StandoutNobel
A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region
1999
Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights
2003 StandoutNobel
QM/MM: what have we learned, where are we, and where do we go from here?
2006
Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase
2003 StandoutNobel
QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone
1996
Enzyme millisecond conformational dynamics do not catalyze the chemical step
2009 StandoutNobel
Proton transfer in the ground and lowest excited states of malonaldehyde: A comparative density functional and post-Hartree–Fock study
1996
Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials
2004
Quantum Mechanical Continuum Solvation Models
2005 Standout
Rational Design of Bisphosphonate Lipid-like Materials for mRNA Delivery to the Bone Microenvironment
2022 StandoutNobel
Mixedab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
1999
How important are entropic contributions to enzyme catalysis?
2000 StandoutNobel
Implementation and validation of the Lacks-Gordon exchange functional in conventional density functional and adiabatic connection methods
1998
An approximate DFT method for QM/MM simulations of biological structures and processes
2003
A discrete solvent reaction field model for calculating frequency-dependent hyperpolarizabilities of molecules in solution
2003
Structure, epr parameters, and reactivity of organic free radicals from a density functional approach
1995
An efficient quantum mechanical/molecular mechanics Monte Carlo simulation of liquid water
2001
QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction
2006
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
1996
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics
2004
Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations
1996
A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)
2002
Theoretical Calculation of the Stark Component of the Solute−Solvent Interaction Energy. Validity of the Mean Field Approximation in the Study of Liquids and Solutions
2002
Theoretical Studies on Alkene Addition to Molybdenum Alkylidenes
1997
Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin
2003 StandoutNobel
A density functional study of the simplest hydrogen abstraction reaction. Effect of self-interaction correction
1994 StandoutNobel
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
Hybrid functionals based on a screened Coulomb potential
2003 Standout
Impact of Pyrophosphate and O-Ethyl-Substituted Pyrophosphate Groups on DNA Structure
2006
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
2010 StandoutNobel
Works of Robert V. Stanton being referenced
Transient Inhibition of ATM Kinase Is Sufficient to Enhance Cellular Sensitivity to Ionizing Radiation
2008
Sequence motifs associated with hepatotoxicity of locked nucleic acid—modified antisense oligonucleotides
2014
Developing predictive assays: The phenotypic screening “rule of 3”
2015
Density functional study of symmetric proton transfers
1994
Density functional transition states of organic and organometallic reactions
1994
An Examination of a Hartree-Fock/Molecular Mechanical Coupled Potential
1995
Identification of small-molecule inhibitors of the JIP–JNK interaction
2009
Quantum Free Energy Perturbation Study within a PM3/MM Coupled Potential
1995
General Formulation for a Quantum Free Energy Perturbation Study
1995
Performance of 3D-Database Molecular Docking Studies into Homology Models
2004
High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields
2009
An examination of a density functional/molecular mechanical coupled potential
1995
Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution
1998
Calculation of solvation free energies using a density functional/molecular dynamics coupled potential
1993