J. J. Ruiz-Pernía

发表

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

I. Tuñón, R. Castillo, V. Moliner, 2012, Chemistry.

Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale DFT/MM Methods

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2020 .

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2020, ACS catalysis.

Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2021, Angewandte Chemie.

A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design†

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2020, Chemical science.

Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies

Israel Sánchez-Moreno, E. García-Junceda, I. Bordes, 2015, International journal of molecular sciences.

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.

I. Tuñón, E. Silla, J. J. Ruiz-Pernía, 2006, Journal of Physical Chemistry B.

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition.

I. Tuñón, V. Moliner, S. Martí, 2012, Journal of chemical theory and computation.

Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.

I. Tuñón, E. Delgado, J. J. Ruiz-Pernía, 2021, Archives of biochemistry and biophysics.

Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.

I. Tuñón, E. Delgado, J. J. Ruiz-Pernía, 2021, Archives of biochemistry and biophysics.

Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2020, ACS catalysis.

Why Are Some Enzymes Dimers? Flexibility and Catalysis in Thermotoga maritima Dihydrofolate Reductase

I. Tuñón, V. Moliner, R. Allemann, 2019, ACS catalysis.

Computational Insights Into Enzyme Catalysis

I. Tuñón, V. Moliner, K. Świderek, 2020 .

On the Nature of the Enzyme–Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study

Julio Caballero, I. Tuñón, J. J. Ruiz-Pernía, 2020, ACS Catalysis.

Enzymatic effects on reactant and transition states. The case of chalcone isomerase.

I. Tuñón, E. Silla, J. J. Ruiz-Pernía, 2007, Journal of the American Chemical Society.

Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions

I. Tuñón, J. J. Ruiz-Pernía, Neyvis Almora‐Barrios, 2019, Chemical science.

Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1

I. Tuñón, Kirill Zinovjev, J. J. Ruiz-Pernía, 2023, ACS catalysis.

Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.

I. Tuñón, J. J. Ruiz-Pernía, Carlos A Ramos-Guzmán, 2021, Chemical communications.

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

I. Tuñón, V. Moliner, M. Roca, 2008, Journal of the American Chemical Society.

A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution.

I. Bordes, R. Castillo, V. Moliner, 2015, Organic & biomolecular chemistry.

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

I. Tuñón, E. Silla, V. Moliner, 2009 .

Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations.

I. Tuñón, Kirill Zinovjev, J. J. Ruiz-Pernía, 2023, Journal of chemical information and modeling.

QM/MM study of l-lactate oxidation by flavocytochrome b2.

F. Lederer, V. Moliner, B. Lévy, 2016, Physical chemistry chemical physics : PCCP.

Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase.

R. Castillo, V. Moliner, M. Roca, 2018, Physical chemistry chemical physics : PCCP.

A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution.

R. Castillo, V. Moliner, J. J. Ruiz-Pernía, 2015, Organic & biomolecular chemistry.

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

Kirill Zinovjev, Iñaki Tuñón, I. Tuñón, 2013, Journal of chemical theory and computation.

Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling

E. Ortí, I. Tuñón, J. Aragó, 2023, Journal of the American Chemical Society.

Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

I. Tuñón, J. Ruiz-Pernía, J. J. Ruiz-Pernía, 2022, Journal of chemical theory and computation.