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A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family

artículo científico publicado en 2019

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA.

artículo científico publicado en 2019

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase

artículo científico publicado en 2016

A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes

artículo científico publicado en 2014

A practical guide to modelling enzyme-catalysed reactions

artículo científico publicado en 2012

A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies

artículo científico publicado en 2011

Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase

artículo científico publicado en 2017

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

artículo científico publicado en 2007

Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study

scientific article published on 01 January 1997

Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex

scientific article published on 14 September 2006

An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases

artículo científico publicado en 2019

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

artículo científico publicado en 2008

Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation

artículo científico publicado en 2013

Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine Dehydrogenase

artículo científico publicado en 2007

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions

artículo científico publicado en 2011

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

artículo científico publicado en 2008

Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase

artículo científico publicado en 2011

Aromatic hydroxylation by cytochrome P450: model calculations of mechanism and substituent effects

artículo científico publicado en 2003

Atomic description of an enzyme reaction dominated by proton tunneling

artículo científico publicado en 2006

BioSimSpace: An interoperable Python framework for biomolecular simulation

scientific article published on 22 November 2019

Biocatalytic Routes to Lactone Monomers for Polymer Production

artículo científico publicado en 2018

Biomolecular simulation and modelling: status, progress and prospects

scientific article published on December 2008

COVID19 - Computational Chemists Meet the Moment

scientific article published on 01 December 2020

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions.

artículo científico publicado en 2007

Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

scientific article published on 01 June 1999

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

artículo científico publicado en 2013

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase

artículo científico publicado en 2014

Comment on "A stationary-wave model of enzyme catalysis" by Carlo Canepa

artículo científico publicado en 2011

Comment on "Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail" by Alexander A. Tulub, Phys. Chem. Chem. Phys., 2006, 8,

artículo científico publicado en 2006

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

artículo científico publicado en 2014

Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate

artículo científico publicado en 2007

Compound I reactivity defines alkene oxidation selectivity in cytochrome P450cam

artículo científico publicado en 2010

Computational and experimental studies on the catalytic mechanism of biliverdin-IXbeta reductase.

artículo científico publicado en 2008

Computational assay of H7N9 influenza neuraminidase reveals R292K mutation reduces drug binding affinity

artículo científico publicado en 2013

Computational enzymology

artículo científico publicado en 2010

Computational enzymology

artículo científico publicado en 2013

Computational enzymology: insight into biological catalysts from modelling

artículo científico publicado en 2008

Computational enzymology: modelling the mechanisms of biological catalysts

artículo científico publicado en 2008

Computer modelling of enzyme catalysed reaction mechanisms.

artículo científico publicado en 1993

Conformational change and ligand binding in the aristolochene synthase catalytic cycle

artículo científico publicado en 2013

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase

artículo científico publicado en 2004

Conformational effects in enzyme catalysis: reaction via a high energy conformation in fatty acid amide hydrolase

artículo científico publicado en 2006

Conformational effects on the pro-S hydrogen abstraction reaction in cyclooxygenase-1: an integrated QM/MM and MD study.

artículo científico publicado en 2013

Constructing ion channels from water-soluble α-helical barrels

artículo científico

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme.

artículo científico publicado en 2017

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations

scientific article published on 01 February 2008

Cyclic boronates as versatile scaffolds for KPC-2 β-lactamase inhibition

artículo científico publicado en 2020

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

artículo científico publicado en 2012

Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.

artículo científico publicado en 2004

Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography

scientific article published on 27 December 2019

Dispelling the effects of a sorceress in enzyme catalysis

artículo científico publicado en 2016

Dissecting the low catalytic capability of flavin-dependent halogenases

artículo científico publicado en 2020

Does compound I vary significantly between isoforms of cytochrome P450?

artículo científico

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

artículo científico publicado en 2018

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

artículo científico publicado en 2012

Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling

scientific article published on 01 September 2005

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study.

artículo científico publicado en 2016

Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme

artículo científico publicado en 2019

Experiment and Simulation Reveal How Mutations in Functional Plasticity Regions Guide Plant Monoterpene Synthase Product Outcome

article

Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

scientific article published in 2021

Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein

scientific article published on 21 September 2020

Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of <i>De Novo</i> Designed Glu/Lys Peptides

artículo científico publicado en 2022

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 beta-lactamase

artículo científico publicado en 2009

High-accuracy computation of reaction barriers in enzymes

artículo científico publicado en 2006

High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase

scientific article published on 20 January 2015

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

artículo científico publicado en 2008

Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems.

artículo científico publicado en 2006

IMPRESSION - prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy

scientific article published on 20 November 2019

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

artículo científico publicado en 2007

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

artículo científico publicado en 2017

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

artículo científico publicado en 2015

Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1

artículo científico publicado en 2017

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

artículo científico publicado en 2009

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

artículo científico publicado en 2020

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

scientific article published on 01 June 2019

Introduction. Biomolecular simulation.

artículo científico publicado en 2008

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.

artículo científico publicado en 2018

Large-Scale Density Functional Theory Transition State Searching in Enzymes

scientific article published on 09 October 2014

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

artículo científico publicado en 2009

Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors

artículo científico publicado en 2019

Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus

artículo científico publicado en 2012

Mechanism and structure-reactivity relationships for aromatic hydroxylation by cytochrome P450.

artículo científico publicado en 2004

Mechanisms of reaction in cytochrome P450: Hydroxylation of camphor in P450cam.

artículo científico publicado en 2006

Modeling protein splicing: reaction pathway for C-terminal splice and intein scission.

artículo científico publicado en 2009

Modelling enzyme reaction mechanisms, specificity and catalysis.

artículo científico publicado en 2005

Molecular Basis of Class A β-Lactamase Inhibition by Relebactam

artículo científico publicado en 2019

Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase

artículo científico publicado en 2007

Molecular dynamics simulations support the hypothesis that the brGDGT paleothermometer is based on homeoviscous adaptation

artículo científico publicado en 2021

Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization

artículo científico publicado en 2005

Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding

artículo científico publicado en 2018

Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance

scientific article published on 30 November 2020

New methods: general discussion.

artículo científico publicado en 2016

Non-adiabatic reactions: general discussion

artículo científico publicado en 2016

Nonempirical energetic analysis of reactivity and covalent inhibition of fatty acid amide hydrolase

artículo científico publicado en 2013

On the Temperature Dependence of Enzyme-Catalyzed Rates

artículo científico publicado en 2016

Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution

scientific article published on 11 March 2019

Protein dynamics and enzyme catalysis: the ghost in the machine?

artículo científico

QM/MM Free-Energy Simulations of Reaction in Serratia marcescens Chitinase B Reveal the Protonation State of Asp142 and the Critical Role of Tyr214

scientific article published on 29 April 2014

QM/MM Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme

article

QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9.

artículo científico publicado en 2008

QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase

artículo científico publicado en 2006

QM/MM modelling of drug-metabolizing enzymes.

artículo científico publicado en 2014

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

artículo científico publicado en 2013

QM/MM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation.

artículo científico publicado en 2005

QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

artículo científico publicado en 2014

QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase

artículo científico publicado en 2005

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

artículo científico publicado en 2019

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2

scientific article published on 10 May 2016

Quantum Mechanics/Molecular Mechanics Modeling of Substrate-Assisted Catalysis in Family 18 Chitinases: Conformational Changes and the Role of Asp142 in Catalysis in ChiB

article

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase

artículo científico publicado en 2017

Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

artículo científico publicado en 2002

Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors

artículo científico publicado en 2013

Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9.

artículo científico publicado en 2013

Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants.

artículo científico publicado en 2017

Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water

artículo científico publicado en 2014

Reaction Mechanism of N -Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, QM/MM Simulation, and Mutagenesis ⬇️

artículo científico publicado en 2014

Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes

artículo científico publicado en 2020

Role of active site residues in promoting cobalt-carbon bond homolysis in adenosylcobalamin-dependent mutases revealed through experiment and computation

artículo científico publicado en 2013

Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-Dehydroshikimate and NADPH Suggest Strategies for MtbSDH Inhibition

scientific article published on 14 March 2019

Simulations of enzymic reactions.

artículo científico publicado en 1996

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.

artículo científico publicado en 2017

Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths

artículo científico publicado en 2010

Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2

artículo científico publicado en 2022

Structural resolution of switchable states of a de novo peptide assembly

artículo científico publicado en 2021

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

artículo científico publicado en 2015

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase

article

Taking Ockham's razor to enzyme dynamics and catalysis

artículo científico publicado en 2012

Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase

artículo científico publicado en 2010

The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail ⬇️

artículo científico publicado en 2016

The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure

artículo científico publicado en 2005

The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations

artículo científico publicado en 2012

The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study

scientific article published on 01 July 2019

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

artículo científico publicado en 2004

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions

artículo científico publicado en 2014

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450.

artículo científico publicado en 2011

Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling

artículo científico publicado en 2011

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

scientific article published on 24 September 2013

Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology

scientific article published on 08 April 2020

“Lethal Synthesis” of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling

scientific article published on 16 September 2011

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