Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
Authors
Keywords
-
Journal
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume 7, Issue 2, Pages e1281
Publisher
Wiley
Online
2016-09-01
DOI
10.1002/wcms.1281
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Reaction Mechanism ofMycobacterium TuberculosisGlutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations
- (2016) Cátia Moreira et al. CHEMISTRY-A EUROPEAN JOURNAL
- Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions
- (2016) Jerônimo Lameira et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant
- (2016) Juan Aranda et al. ACS Catalysis
- QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase
- (2016) Eduardo F. Oliveira et al. Catalysis Science & Technology
- New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models
- (2015) Gaspar P. Pinto et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- The ONIOM Method and Its Applications
- (2015) Lung Wa Chung et al. CHEMICAL REVIEWS
- Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
- (2015) Elizabeth Brunk et al. CHEMICAL REVIEWS
- Theoretical study of the reaction mechanism of phenolic acid decarboxylase
- (2015) Xiang Sheng et al. FEBS Journal
- High-Level QM/MM Calculations Support the Concerted Mechanism for Michael Addition and Covalent Complex Formation in Thymidylate Synthase
- (2015) Nopporn Kaiyawet et al. Journal of Chemical Theory and Computation
- Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems
- (2015) Pandian Sokkar et al. Journal of Chemical Theory and Computation
- Establishing the Catalytic Mechanism of Human Pancreatic α-Amylase with QM/MM Methods
- (2015) Gaspar P. Pinto et al. Journal of Chemical Theory and Computation
- Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study
- (2015) Manju Kumari et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase
- (2015) Keyarash Sadeghian et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The working mechanism of the β-carbonic anhydrase degrading carbonyl sulphide (COSase): a theoretical study
- (2015) P. Piazzetta et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations
- (2015) Rui P. P. Neves et al. ACS Catalysis
- Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases
- (2015) Sérgio F. Sousa et al. ACS Catalysis
- Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease
- (2015) António J. M. Ribeiro et al. ACS Catalysis
- Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase
- (2015) António J. M. Ribeiro et al. ACS Catalysis
- Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B)
- (2015) Hisham M. Dokainish et al. ACS Catalysis
- Role of Substrate Dynamics in Protein Prenylation Reactions
- (2014) Dhruva K. Chakravorty et al. ACCOUNTS OF CHEMICAL RESEARCH
- Using Quantum Mechanical Approaches to Study Biological Systems
- (2014) Kenneth M. Merz ACCOUNTS OF CHEMICAL RESEARCH
- Quantum Chemical Studies of Mechanisms for Metalloenzymes
- (2014) Margareta R. A. Blomberg et al. CHEMICAL REVIEWS
- Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase
- (2014) Jiayun Pang et al. CHEMISTRY-A EUROPEAN JOURNAL
- Averaging Techniques for Reaction Barriers in QM/MM Simulations
- (2014) April M. Cooper et al. CHEMPHYSCHEM
- Enzymatic “tricks”: Carboxylate shift and sulfur shift
- (2014) Sérgio F. Sousa et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations
- (2014) Ana R. Araújo et al. Journal of Chemical Theory and Computation
- Benchmarking of Density Functionals for the Accurate Description of Thiol–Disulfide Exchange
- (2014) Rui P. P. Neves et al. Journal of Chemical Theory and Computation
- Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase
- (2014) Tobias Schmidt et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Large-Scale Density Functional Theory Transition State Searching in Enzymes
- (2014) Greg Lever et al. Journal of Physical Chemistry Letters
- A Mechanistic Study of the Lewis Base-Directed Cycloaddition of 2-Pyrones and Alkynylboranes
- (2014) Damien F. P. Crépin et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations
- (2014) Ana R. Calixto et al. ACS Catalysis
- QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme
- (2014) Natércia F. Brás et al. ACS Catalysis
- Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case
- (2013) Maria E. S. Lind et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover
- (2013) Lauren C. McGowan et al. BIOPHYSICAL JOURNAL
- The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations
- (2013) António J. M. Ribeiro et al. CHEMISTRY-A EUROPEAN JOURNAL
- Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes
- (2013) Sérgio F. Sousa et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Conformational Compression and Barrier Height Heterogeneity in the N-Acetylglutamate Kinase
- (2013) Melchor Sanchez-Martinez et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Mechanism and Selectivity of Rhodium-Catalyzed 1:2 Coupling of Aldehydes and Allenes
- (2013) Genping Huang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Amine Oxidation Mediated by Lysine-Specific Demethylase 1: Quantum Mechanics/Molecular Mechanics Insights into Mechanism and Role of Lysine 661
- (2013) Bora Karasulu et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Base-Pairing Energies of Proton-Bound Heterodimers of Cytosine and Modified Cytosines: Implications for the Stability of DNA i-Motif Conformations
- (2013) Bo Yang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Unraveling the Enigmatic Mechanism of l-Asparaginase II with QM/QM Calculations
- (2013) Diana S. Gesto et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Oxygen activation by homoprotocatechuate 2,3-dioxygenase: a QM/MM study reveals the key intermediates in the activation cycle
- (2013) Geng Dong et al. Chemical Science
- Protein dynamics and enzyme catalysis: the ghost in the machine?
- (2012) David R. Glowacki et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- A practical guide to modelling enzyme-catalysed reactions
- (2012) Richard Lonsdale et al. CHEMICAL SOCIETY REVIEWS
- Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa
- (2012) Tiziana Marino et al. CHEMISTRY-A EUROPEAN JOURNAL
- Development of Polyphenols as HIV-1 Integrase Inhibitors: a Summary and Perspective
- (2012) S. Yu et al. CURRENT MEDICINAL CHEMISTRY
- A density functional theory investigation on the formation mechanisms of DNA interstrand crosslinks induced by chloroethylnitrosoureas
- (2012) Li-Jiao Zhao et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase
- (2012) Rong-Zhen Liao et al. Journal of Chemical Theory and Computation
- Exploring, Refining, and Validating the Paradynamics QM/MM Sampling
- (2012) Nikolay V. Plotnikov et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations
- (2012) António J. M. Ribeiro et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The catalytic mechanism of mouse renin studied with QM/MM calculations
- (2012) Natércia F. Brás et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
- (2012) Jimmy Heimdal et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers
- (2012) Sérgio Filipe Sousa et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Resolving the complex role of enzyme conformational dynamics in catalytic function
- (2012) U. Doshi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls
- (2012) Pedro J. Silva et al. THEORETICAL CHEMISTRY ACCOUNTS
- The Catalytic Mechanism of RNA Polymerase II
- (2011) Alexandra T. P. Carvalho et al. Journal of Chemical Theory and Computation
- The Accuracy of Density Functional Theory in the Description of Cation−π and π–Hydrogen Bond Interactions
- (2011) Ana Rute Neves et al. Journal of Chemical Theory and Computation
- Effect of the damping function in dispersion corrected density functional theory
- (2011) Stefan Grimme et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA
- (2011) Óscar Passos et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks
- (2011) Nikolay V. Plotnikov et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
- (2011) Edina Rosta et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes
- (2011) Eduardo F. Oliveira et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Multiscale modeling of biological functions
- (2011) Shina Caroline Lynn Kamerlin et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions
- (2011) Lars Goerigk et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Theoretical insights into the catalytic mechanism of β-hexosaminidase
- (2011) Óscar Passos et al. THEORETICAL CHEMISTRY ACCOUNTS
- Computational enzymology
- (2010) Richard Lonsdale et al. CHEMICAL COMMUNICATIONS
- Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods
- (2010) Kara E. Ranaghan et al. INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY
- A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
- (2010) Stefan Grimme et al. JOURNAL OF CHEMICAL PHYSICS
- Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2′- Deoxy-2′-methylenecytidine-5′-diphosphate
- (2010) M. A. S. Perez et al. Journal of Chemical Theory and Computation
- QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions
- (2010) Natércia F. Brás et al. Journal of Chemical Theory and Computation
- Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths
- (2010) Alessio Lodola et al. Journal of Chemical Theory and Computation
- Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds
- (2010) António J. M. Ribeiro et al. Journal of Chemical Theory and Computation
- Thorpe−Ingold Acceleration of Oxirane Formation Is Mostly a Solvent Effect
- (2010) Jakub Kostal et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations
- (2010) R.-Z. Liao et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- QM/MM Methods for Biomolecular Systems
- (2009) Hans Martin Senn et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase
- (2009) Sérgio Filipe Sousa et al. CHEMISTRY-A EUROPEAN JOURNAL
- Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
- (2009) Per E. M. Siegbahn et al. JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
- Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes
- (2009) Sérgio F. Sousa et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- DFT studies on the β-glycosidase catalytic mechanism: The deglycosylation step
- (2009) Natércia F. Brás et al. JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM
- Computational Enzymatic Catalysis
- (2008) Maria J. Ramos et al. ACCOUNTS OF CHEMICAL RESEARCH
- Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
- (2008) Hao Hu et al. Annual Review of Physical Chemistry
- Computational enzymology: modelling the mechanisms of biological catalysts: Figure 1
- (2008) Adrian J. Mulholland BIOCHEMICAL SOCIETY TRANSACTIONS
- Free-Energy Landscape of Enzyme Catalysis†
- (2008) Stephen J. Benkovic et al. BIOCHEMISTRY
- Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems
- (2008) Yan Zhang et al. Journal of Chemical Theory and Computation
- Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates
- (2008) Natércia F. Brás et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computational enzymology: insight into biological catalysts from modelling
- (2008) Marc W. van der Kamp et al. NATURAL PRODUCT REPORTS
- On the relationship between folding and chemical landscapes in enzyme catalysis
- (2008) M. Roca et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now