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Peek at the Potential Energy Surfaces of the LSSmKate1 and LSSmKate2 Proteins

The journal of physical chemistry. B, 2012-12, Vol.116 (49), p.14302-14310

2012

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A QM/MM study of Kemptide phosphorylation catalyzed by protein kinase A. The role of Asp166 as a general acid/base catalyst

Physical chemistry chemical physics : PCCP, 2015-01, Vol.17 (5), p.3497-3511

2015

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How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima?

Journal of chemical theory and computation, 2013-03, Vol.9 (3), p.1731-1742

2013

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Unraveling how the Gly526Ser mutation arrests prostaglandin formation from arachidonic acid catalyzed by cyclooxygenase-2: a combined molecular dynamics and QM/MM study

RSC advances, 2020-01, Vol.1 (2), p.986-997

2020

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A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2

Organic & biomolecular chemistry, 2014-05, Vol.12 (17), p.2645-2655

2014

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Molecular Insights into the Regulation of 3‑Phosphoinositide-Dependent Protein Kinase 1: Modeling the Interaction between the Kinase and the Pleckstrin Homology Domains

ACS omega, 2022-07, Vol.7 (29), p.25186-25199

2022

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Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study

Frontiers in chemistry, 2019-04, Vol.7, p.200-200

2019

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Tunneling in Green Tea: Understanding the Antioxidant Activity of Catechol-Containing Compounds. A Variational Transition-State Theory Study

Journal of the American Chemical Society, 2007-05, Vol.129 (18), p.5846-5854

2007

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Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+ and Sr2+: a QM/MM study

Physical chemistry chemical physics : PCCP, 2017-04, Vol.19 (16), p.10377-10394

2017

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Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

The journal of physical chemistry. B, 2008-05, Vol.112 (17), p.5500-5511

2008

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Theoretical Computer-Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F

Chemphyschem, 2015-07, Vol.16 (10), p.2134-2139

2015

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New insights into the structure-spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment

Organic & biomolecular chemistry, 2014-12, Vol.12 (48), p.9845-9852

2014

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Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

Physical chemistry chemical physics : PCCP, 2015-01, Vol.17 (43), p.29363-29373

2015

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A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant

Journal of computer-aided molecular design, 2014-11, Vol.28 (11), p.1077-1091

2014

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Introducing Mutations to Modify the C13/C9 Ratio in Linoleic Acid Oxygenations Catalyzed by Rabbit 15-Lipoxygenase: A QM/MM and MD Study

Chemphyschem, 2014-12, Vol.15 (18), p.4049-4054

2014

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QM/MM Studies Reveal How Substrate-Substrate and Enzyme-Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism

Advances in protein chemistry and structural biology, 2015, Vol.100, p.225-254

2015

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Exploring the Effects of Intramolecular Vibrational Energy Redistribution on the Operation of the Proton Wire in Green Fluorescent Protein

The journal of physical chemistry. B, 2008-10, Vol.112 (42), p.13443-13452

2008

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On the Regio- and Stereospecificity of Arachidonic Acid Peroxidation Catalyzed by Mammalian 15-Lypoxygenases: A Combined Molecular Dynamics and QM/MM Study

Chemphyschem, 2013-11, Vol.14 (16), p.3777-3787

2013

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Synthetic Photoswitchable Neurotransmitters Based on Bridged Azobenzenes

Organic letters, 2019-05, Vol.21 (10), p.3780-3784

2019

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Rationally designed azobenzene photoswitches for efficient two-photon neuronal excitation

Nature communications, 2019-02, Vol.10 (1), p.907-907, Article 907

2019

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A Potential Energy Function for Heterogeneous Proton-Wires. Ground and Photoactive States of the Proton-Wire in the Green Fluorescent Protein

Journal of chemical theory and computation, 2008-07, Vol.4 (7), p.1138-1150

2008

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Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer Process in the Green Fluorescent Protein: Classical Molecular Dynamics and Multiconfigurational Electronic Structure Calculations

Journal of the American Chemical Society, 2006-03, Vol.128 (11), p.3564-3574

2006

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A QM/MM study of the phosphoryl transfer to the Kemptide substrate catalyzed by protein kinase A. The effect of the phosphorylation state of the protein on the mechanism

Physical chemistry chemical physics : PCCP, 2011-01, Vol.13 (2), p.53-539

2011

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Substrate binding to mammalian 15-lipoxygenase

Journal of computer-aided molecular design, 2011-09, Vol.25 (9), p.825-835

2011

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N‑Substituted 5‑(1H‑Indol-2-yl)-2-methoxyanilines Are Allosteric Inhibitors of the Linoleate Oxygenase Activity of Selected Mammalian ALOX15 Orthologs: Mechanism of Action

Journal of medicinal chemistry, 2022-02, Vol.65 (3), p.1979-1995

2022

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Peek at the Potential Energy Surfaces of the LSSmKate1 and LSSmKate2 Proteins

A QM/MM study of Kemptide phosphorylation catalyzed by protein kinase A. The role of Asp166 as a general acid/base catalyst

How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima?

Unraveling how the Gly526Ser mutation arrests prostaglandin formation from arachidonic acid catalyzed by cyclooxygenase-2: a combined molecular dynamics and QM/MM study

A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2

Molecular Insights into the Regulation of 3‑Phosphoinositide-Dependent Protein Kinase 1: Modeling the Interaction between the Kinase and the Pleckstrin Homology Domains

Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study

Tunneling in Green Tea: Understanding the Antioxidant Activity of Catechol-Containing Compounds. A Variational Transition-State Theory Study

Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+ and Sr2+: a QM/MM study

Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

Theoretical Computer-Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F

New insights into the structure-spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment

Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein

A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant

Introducing Mutations to Modify the C13/C9 Ratio in Linoleic Acid Oxygenations Catalyzed by Rabbit 15-Lipoxygenase: A QM/MM and MD Study

QM/MM Studies Reveal How Substrate-Substrate and Enzyme-Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism

Exploring the Effects of Intramolecular Vibrational Energy Redistribution on the Operation of the Proton Wire in Green Fluorescent Protein

On the Regio- and Stereospecificity of Arachidonic Acid Peroxidation Catalyzed by Mammalian 15-Lypoxygenases: A Combined Molecular Dynamics and QM/MM Study

Synthetic Photoswitchable Neurotransmitters Based on Bridged Azobenzenes

Rationally designed azobenzene photoswitches for efficient two-photon neuronal excitation

A Potential Energy Function for Heterogeneous Proton-Wires. Ground and Photoactive States of the Proton-Wire in the Green Fluorescent Protein

Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer Process in the Green Fluorescent Protein: Classical Molecular Dynamics and Multiconfigurational Electronic Structure Calculations

A QM/MM study of the phosphoryl transfer to the Kemptide substrate catalyzed by protein kinase A. The effect of the phosphorylation state of the protein on the mechanism

Substrate binding to mammalian 15-lipoxygenase

N‑Substituted 5‑(1H‑Indol-2-yl)-2-methoxyanilines Are Allosteric Inhibitors of the Linoleate Oxygenase Activity of Selected Mammalian ALOX15 Orthologs: Mechanism of Action

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