Search

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

401

Downloads

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

615

Downloads

1

Citations

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

145

Downloads

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

262

Downloads

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

681

Downloads

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

293

Downloads

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

192

Downloads

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 4 posted 18 March 2025

211

Downloads

Theoretical and Computational Chemistry

Working Paper

Multi-objective evolutionary strategy for improving semiempirical Hamiltonians in the study of enzymatic reactions at the QM/MM level of theory

José Luís Velázquez-Libera, Rodrigo Recabarren, Esteban Vöhringer-Martinez, Yamisleydi Salgueiro, J. Javier Ruiz-Pernía, Julio Caballero, Iñaki Tuñón

Version 1 posted 13 February 2025

59

Downloads

Refine Search

9 results in J. Javier Ruiz-Pernia in Authors: J. Javier Ruiz-Pernia

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

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

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

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

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

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

Multi-objective evolutionary strategy for improving semiempirical Hamiltonians in the study of enzymatic reactions at the QM/MM level of theory

9 results in Authors: J. Javier Ruiz-Pernia