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Biological and Medicinal Chemistry

Working Paper

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

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 08 December 2020

654

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Biological and Medicinal Chemistry

Working Paper

Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 26 March 2021

587

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1

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Theoretical and Computational Chemistry

Working Paper

Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism

Jorge Pardos, Adrián García-Martínez, J. Javier Ruiz-Pernia, Iñaki Tuñón

Version 1 posted 06 November 2024

108

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Theoretical and Computational Chemistry

Working Paper

A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms

Johanna Schillings, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 17 January 2024

232

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Biological and Medicinal Chemistry

Working Paper

Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatases

Kirill Zinovjev, Paul Guénon, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón

Version 1 posted 03 July 2023

361

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Theoretical and Computational Chemistry

Working Paper

Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

Adrián García-Martínez, Kirill Zinovjev, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 02 August 2023

155

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Theoretical and Computational Chemistry

Working Paper

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

Carlos A. Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 23 November 2022

263

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Theoretical and Computational Chemistry

Working Paper

Adapted DFTB3 repulsive potentials reach DFT accuracy for hydride transfer reactions in enzymes

José Luís Velázquez-Libera, Rodrigo Recabarren, David Adrian Saez, Carlos Castillo, J. Javier Ruiz-Pernía, Iñaki Tuñón, Esteban Vöhringer-Martinez

Version 3 posted 17 December 2024

83

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8 results in J. Javier Ruiz-Pernía in Authors: J. Javier Ruiz-Pernía

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

Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism

A Computational Comparison Between Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease. Implications for Resistance Mechanisms

Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatases

Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

Adapted DFTB3 repulsive potentials reach DFT accuracy for hydride transfer reactions in enzymes

8 results in Authors: J. Javier Ruiz-Pernía