Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling

(2009) Alessio Lodola et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Peroxide-Dependent Formation of a Covalent Link between Trp51 and the Heme in CytochromecPeroxidase†

(2009) Zoi Pipirou et al.   BIOCHEMISTRY

An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling

(2009) Judith P. Klinman   CHEMICAL PHYSICS LETTERS

Docking-Based Virtual Screening: Recent Developments

(2009) Tiziano Tuccinardi   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Computational evaluation of protein–small molecule binding

(2009) Olgun Guvench et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-Based Drug Design Strategies in Medicinal Chemistry

(2009) Adriano Andricopulo et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Targeted scoring functions for virtual screening

(2009) Markus H.J. Seifert   DRUG DISCOVERY TODAY

Recent developments of the quantum chemical cluster approach for modeling enzyme reactions

(2009) Per E. M. Siegbahn et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease

(2009) Pedro Fong et al.   Journal of Chemical Information and Modeling

QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena?

(2009) M. Paul Gleeson et al.   Journal of Chemical Information and Modeling

QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism

(2009) Li Tian et al.   Journal of Chemical Theory and Computation

Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

(2009) Ming-Hsun Ho et al.   Journal of Chemical Theory and Computation

Lennard−Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases

(2009) Ulla Pentikäinen et al.   Journal of Chemical Theory and Computation

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A β-Lactamase†

(2009) Johannes C. Hermann et al.   JOURNAL OF PHYSICAL CHEMISTRY A

What Kinds of Ferryl Species Exist for Compound II of Chloroperoxidase? A Dialog of Theory with Experiment

(2009) Wenzhen Lai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fixation of the Two Tabun Isomers in Acetylcholinesterase: A QM/MM Study

(2009) Ophélie Kwasnieski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

(2009) Luis Petersen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations

(2009) Katherine E. Shaw et al.   Journal of Physical Chemistry Letters

How the Substrated-Glutamate Drives the Catalytic Action ofBacillus subtilisGlutamate Racemase

(2009) Eduard Puig et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How is the Reactivity of Cytochrome P450cam Affected by Thr252X Mutation? A QM/MM Study for X = Serine, Valine, Alanine, Glycine

(2009) Muhannad Altarsha et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reductive Half-Reaction of Aldehyde Oxidoreductase toward Acetaldehyde: A Combined QM/MM Study

(2009) Sebastian Metz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Mitogen-Activated Protein Kinases Recognize and Phosphorylate Their Targets: A QM/MM Study

(2009) Adrian Gustavo Turjanski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalyzing Racemizations in the Absence of a Cofactor: The Reaction Mechanism in Proline Racemase

(2009) Amir Rubinstein et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site

(2009) Prasad Phatak et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theoretical and Experimental Studies of the Conversion of Chromopyrrolic Acid to an Antitumor Derivative by Cytochrome P450 StaP: The Catalytic Role of Water Molecules

(2009) Yong Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Spectroscopic and Kinetic Evidence on How Bacteriorhodopsin Accomplishes Vectorial Proton Transport under Functional Conditions

(2009) Víctor A. Lórenz-Fonfría et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational Variability of Benzamidinium-Based Inhibitors

(2009) Xue Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2

(2009) Adam J. T. Smith et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate

(2008) Anna L. Bowman et al.   CHEMICAL COMMUNICATIONS

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase

(2008) Marc W. van der Kamp et al.   CHEMICAL COMMUNICATIONS

Glutathione Transferase: New Model for Glutathione Activation

(2008) Daniel F. A. R. Dourado et al.   CHEMISTRY-A EUROPEAN JOURNAL

Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin

(2008) Marcel Baer et al.   CHEMPHYSCHEM

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Limitations and lessons in the use of X-ray structural information in drug design

(2008) A DAVIS et al.   DRUG DISCOVERY TODAY

Plenary Lectures

(2008)   FEBS Journal

Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase

(2008) Toyokazu Ishida   JOURNAL OF CHEMICAL PHYSICS

Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase

(2008) Ricardo A. Mata et al.   JOURNAL OF CHEMICAL PHYSICS

Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization

(2008) Yang Yang et al.   Journal of Chemical Theory and Computation

Role of structural water molecule in HIV protease-inhibitor complexes: A QM/MM study

(2008) Cherumuttathu H. Suresh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin

(2008) Yang Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

A dynamic view of enzyme catalysis

(2008) Aurora Jiménez et al.   JOURNAL OF MOLECULAR MODELING

A QM/MM study of the reaction mechanism for the 3′-processing step catalyzed by HIV-1 integrase

(2008) J. Javier Ruiz-Pernía et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Electron Transfer in the P450cam/PDX Complex. The QM/MM e-Pathway†

(2008) Frank Wallrapp et al.   JOURNAL OF PHYSICAL CHEMISTRY A

QM/MM Modeling of Benzene Hydroxylation in Human Cytochrome P450 2C9†

(2008) Christine M. Bathelt et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Comparison Studies of the Human Heart andBacillus stearothermophilusLactate Dehydrogreanse by Transition Path Sampling†

(2008) Sara L. Quaytman et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Origin of the Activity Drop with the E50D Variant of Catalytic Antibody 34E4 for Kemp Elimination

(2008) Anastassia N. Alexandrova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting an Improvement of Secondary Catalytic Activity of Promiscuos Isochorismate Pyruvate Lyase by Computational Design

(2008) Sergio Martí et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bond or Cage Effect:  How Nitrophorins Transport and Release Nitric Oxide

(2008) Marcelo A. Martí et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination

(2008) Anastassia N. Alexandrova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biomolecular simulation and modelling: status, progress and prospects

(2008) M. W van der Kamp et al.   Journal of the Royal Society Interface

Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds

(2008) K. Senthilkumar et al.   Journal of the Royal Society Interface

The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase

(2008) C. J. R. Illingworth et al.   MOLECULAR PHYSICS

Computational enzymology: insight into biological catalysts from modelling

(2008) Marc W. van der Kamp et al.   NATURAL PRODUCT REPORTS

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Do-it-yourself enzymes

(2008) Vikas Nanda   Nature Chemical Biology

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Combined QM/MM mechanistic study of the acylation process in furin complexed with the H5N1 avian influenza virus hemagglutinin's cleavage site

(2008) Thanyada Rungrotmongkol et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling

(2007) Alessio Lodola et al.   CHEMICAL COMMUNICATIONS