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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

626

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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

142

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Theoretical and Computational Chemistry

Working Paper

Molecular mechanism of rRNA maturation by M5: interplay between conformational flexibility and reactivity

Julie Puyo-Fourtine, Laetitia Kantin, Milorad Andelkovic, Carine Tisné, Elisa Frezza, Inaki Tunon, Elise Duboué-Dijon

Version 1 posted 23 September 2024

40

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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

342

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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

858

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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

549

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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

870

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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

251

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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

1,113

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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

202

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1

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Refine Search

14 results in Iñaki Tuñon in Authors: Iñaki Tuñon

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

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

Molecular mechanism of rRNA maturation by M5: interplay between conformational flexibility and reactivity

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

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

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

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

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

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

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

14 results in Authors: Iñaki Tuñon