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Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases

Molecules (Basel, Switzerland), 2022-10, Vol.27 (20), p.7031

2022

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Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling

Molecules (Basel, Switzerland), 2021-04, Vol.26 (7), p.2026

2021

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Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling

International journal of molecular sciences, 2022-12, Vol.24 (1), p.176

2022

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Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Physical chemistry chemical physics : PCCP, 2018, Vol.20 (37), p.23827-23836

2018

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Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

Molecules (Basel, Switzerland), 2021-10, Vol.26 (20), p.6280

2021

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Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

Molecules (Basel, Switzerland), 2021-06, Vol.26 (13), p.3998

2021

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KuINins as a New Class of HIV-1 Inhibitors That Block Post-Integration DNA Repair

International journal of molecular sciences, 2023-12, Vol.24 (24), p.17354

2023

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Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

Journal of computational chemistry, 2016-07, Vol.37 (19), p.1801-1809

2016

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The role of the correlated motion(s) of the chromophore in photoswitching of green and red forms of the photoconvertible fluorescent protein mSAASoti

Scientific reports, 2024-04, Vol.14 (1), p.8754-8754, Article 8754

2024

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Saturation Mutagenesis and Molecular Modeling: The Impact of Methionine 182 Substitutions on the Stability of β-Lactamase TEM-1

International journal of molecular sciences, 2024-07, Vol.25 (14), p.7691

2024

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The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules (Basel, Switzerland), 2021-08, Vol.26 (16), p.5053

2021

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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Proceedings of the National Academy of Sciences - PNAS, 2020-03, Vol.117 (10), p.5280-5290

2020

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Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate

Biochemistry (Easton), 2014-11, Vol.53 (45), p.7093-7099

2014

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Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form

International journal of molecular sciences, 2023-04, Vol.24 (9), p.7906

2023

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To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense

Molecules (Basel, Switzerland), 2023-02, Vol.28 (5), p.2109

2023

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Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore

The journal of physical chemistry. B, 2011-06, Vol.115 (25), p.8296-8303

2011

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LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift

International journal of molecular sciences, 2021-11, Vol.22 (23), p.12887

2021

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Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections

International journal of molecular sciences, 2022-02, Vol.23 (3), p.1834

2022

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Monomerization of the photoconvertible fluorescent protein SAASoti by rational mutagenesis of single amino acids

Scientific reports, 2018-10, Vol.8 (1), p.15542-14, Article 15542

2018

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Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors

Physical chemistry chemical physics : PCCP, 2020-09, Vol.22 (34), p.1969-1979

2020

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Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

Journal of chemical information and modeling, 2022-12, Vol.62 (24), p.6519-6529

2022

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A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine

Crystals (Basel), 2022-05, Vol.12 (5), p.619

2022

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The explicit role of electron exchange in the hydrogen bonded molecular complexes

Journal of computational chemistry, 2021-05, Vol.42 (12), p.870-882

2021

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Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

Journal of chemical information and modeling, 2021-03, Vol.61 (3), p.1215-1225

2021

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Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes

The journal of physical chemistry. B, 2019-07, Vol.123 (29), p.6133-6149

2019

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Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases

Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling

Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

KuINins as a New Class of HIV-1 Inhibitors That Block Post-Integration DNA Repair

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

The role of the correlated motion(s) of the chromophore in photoswitching of green and red forms of the photoconvertible fluorescent protein mSAASoti

Saturation Mutagenesis and Molecular Modeling: The Impact of Methionine 182 Substitutions on the Stability of β-Lactamase TEM-1

The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate

Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form

To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense

Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore

LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift

Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections

Monomerization of the photoconvertible fluorescent protein SAASoti by rational mutagenesis of single amino acids

Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine

The explicit role of electron exchange in the hydrogen bonded molecular complexes

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes

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