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Theoretical and Computational Chemistry

Working Paper

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

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

Version 2 posted 07 July 2020

1,137

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Theoretical and Computational Chemistry

Working Paper

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

Rodrigo Recabarren, Kirill Zinovjev, Iñaki Tuñón, Jans Alzate-Morales

Version 1 posted 01 July 2020

903

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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

86

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Biological and Medicinal Chemistry

Working Paper

Binding and Reactivity of a Nitrile Oral Inhibitor of SARS-CoV-2 Main Protease Revealed by Computational Simulations

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

Version 1 posted 23 July 2021

874

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Theoretical and Computational Chemistry

Working Paper

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W. van der Kamp

Version 2 posted 27 February 2024

736

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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

235

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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

156

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Theoretical and Computational Chemistry

Working Paper

The competing reaction mechanisms of peptide bond formation in water revealed by deep potential molecular dynamics and path sampling

Rolf David, Iñaki Tuñón, Damien Laage

Version 1 posted 19 March 2024

561

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1

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Biological and Medicinal Chemistry

Working Paper

Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig L-Asparaginase Type 1 for Leukemia Drug Design

Milorad Andjelkovic, Kirill Zinovjev, Jose Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 18 December 2024

54

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Theoretical and Computational Chemistry

Working Paper

Catalytic Reaction Mechanism in Native and Mutant COMT from the Adaptive String Method and Mean Reaction Force Analysis.

David Adrian Saez, Kirill Zinovjev, Iñaki Tuñon, Esteban Vöhringer-Martinez

Version 1 posted 10 May 2018

573

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18 results in Iñaki Tuñon in Authors: Iñaki Tuñon

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

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

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

Binding and Reactivity of a Nitrile Oral Inhibitor of SARS-CoV-2 Main Protease Revealed by Computational Simulations

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

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

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

The competing reaction mechanisms of peptide bond formation in water revealed by deep potential molecular dynamics and path sampling

Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig L-Asparaginase Type 1 for Leukemia Drug Design

Catalytic Reaction Mechanism in Native and Mutant COMT from the Adaptive String Method and Mean Reaction Force Analysis.

18 results in Authors: Iñaki Tuñon