Iñaki Tuñón

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 39

Top Topics

Molecular Dynamics Simulations

Top Venues

Chemical science

Journal of chemical information and modeling

Journal of chemical theory and computation

Journal of the American Chemical Society

This page only lists publications with an associated author ORCID identifier.

Publications

Kirill Zinovjev, Paul Guénon, Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón
Activation and friction in enzymatic loop opening and closing dynamics. Nature communications 15 (1) (2024)
Rolf David, Iñaki Tuñón, Damien Laage
Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. Journal of the American Chemical Society 146 (20) (2024)
José Luis Velázquez-Libera, Julio Caballero, Jans H Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. Journal of chemical information and modeling 64 (10) (2024)
Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W Van der Kamp
emle-engine : A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (11) (2024)
Rolf David, Iñaki Tuñón, Damien Laage
Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. Journal of the American Chemical Society (2024)
José Luis Velázquez-Libera, Julio Caballero, Jans H Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. Journal of chemical information and modeling 64 (10) (2024)
Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W Van der Kamp
emle-engine : A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (11) (2024)
Kirill Zinovjev, Paul Guénon, Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón
Activation and friction in enzymatic loop opening and closing dynamics. Nature communications 15 (1) (2024)
José Luis Velázquez-Libera, Julio Caballero, Jans H Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. Journal of chemical information and modeling (2024)
Kirill Zinovjev, Paul Guénon, Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón
Activation and friction in enzymatic loop opening and closing dynamics. Nature communications 15 (1) (2024)
Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W Van der Kamp
emle-engine : A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. Journal of chemical theory and computation (2024)
Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W Van der Kamp
emle-engine : A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (11) (2024)
Adrián García-Martínez, Kirill Zinovjev, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations. Journal of the American Chemical Society (2023)
Carlos Alberto Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, Jose Javier Ruiz-Pernía, Iñaki Tuñón
The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Chemical science 14 (10) (2023)
Carlos Alberto Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, Jose Javier Ruiz-Pernía, Iñaki Tuñón
The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Chemical science 14 (10) (2023)
Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Kirill Zinovjev, Iñaki Tuñón
Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1. ACS catalysis 13 (7) (2023)
Rafael García-Meseguer, Enrique Ortí, Iñaki Tuñón, Jose Javier Ruiz-Pernía, Juan Aragó
Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling. Journal of the American Chemical Society (2023)
Milorad Andjelkovic, Kirill Zinovjev, Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations. Journal of chemical information and modeling (2023)
Abdelazim M A Abdelgawwad, Antonio Monari, Iñaki Tuñón, Antonio Francés-Monerris
Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative. Journal of chemical information and modeling 62 (13) (2022)
Carlos A Ramos-Guzmán, José Luis Velázquez-Libera, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition. Journal of chemical theory and computation 18 (6) (2022)
Kevin Blanco-Esperguez, Iñaki Tuñón, Johannes Kästner, Fernando Mendizábal, Sebastián Miranda-Rojas
Unraveling the Role of the Tyrosine Tetrad from the Binding Site of the Epigenetic Writer MLL3 in the Catalytic Mechanism and Methylation Multiplicity. International journal of molecular sciences 23 (18) (2022)
Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs*. Angewandte Chemie (International ed. in English) 60 (49) (2021)
Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón
Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease. Chemical communications (Cambridge, England) 57 (72) (2021)
Carlos Alberto Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón
A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design. Chemical science 12 (10) (2021)
Sebastián Miranda-Rojas, Kevin Blanco-Esperguez, Iñaki Tuñón, Johannes Karwounopoulos, Fernando Mendizábal
Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study. Biomolecules 11 (7) (2021)
María Gálvez-Llompart, Riccardo Ocello, Laura Rullo, Serena Stamatakos, Irene Alessandrini, Riccardo Zanni, Iñaki Tuñón, Andrea Cavalli, Sanzio Candeletti, Matteo Masetti, Patrizia Romualdi, Maurizio Recanatini
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. Journal of chemical information and modeling 61 (6) (2021)
Agata Sowińska, Luis Vasquez, Szymon Żaczek, Rabindra Nath Manna, Iñaki Tuñón, Agnieszka Dybala-Defratyka
Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA. The journal of physical chemistry. B 124 (46) (2020)
José Navarro-Sánchez, Neyvis Almora-Barrios, Belén Lerma-Berlanga, Jose Javier Ruiz-Pernía, Victor A Lorenz-Fonfria, Iñaki Tuñón, Carlos Martí-Gastaldo
Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions. Chemical science 10 (14) (2019)
Antonio Francés-Monerris, Iñaki Tuñón, Antonio Monari
Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment. The journal of physical chemistry letters 10 (21) (2019)
Juliana Murillo-López, Kirill Zinovjev, Humberto Pereira, Andres Caniuguir, Richard Garratt, Jorge Babul, Rodrigo Recabarren, Jans Alzate-Morales, Julio Caballero, Iñaki Tuñón, Ricardo Cabrera
Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations. Chemical science 10 (10) (2019)
Lorena E Rosaleny, Kirill Zinovjev, Iñaki Tuñón, Alejandro Gaita-Ariño
A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules. Physical chemistry chemical physics : PCCP 21 (21) (2019)
Antonio Francés-Monerris, Hugo Gattuso, Daniel Roca-Sanjuán, Iñaki Tuñón, Marco Marazzi, Elise Dumont, Antonio Monari
Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA. Chemical science 9 (41) (2018)
Katarzyna Świderek, Iñaki Tuñón, Ian H Williams, Vicent Moliner
Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling. Journal of the American Chemical Society 140 (12) (2018)
David Adrian Saez, Kirill Zinovjev, Iñaki Tuñón, Esteban Vöhringer-Martinez
Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. The journal of physical chemistry. B 122 (38) (2018)
Kirill Zinovjev, Iñaki Tuñón
Quantifying the limits of transition state theory in enzymatic catalysis. Proceedings of the National Academy of Sciences of the United States of America 114 (47) (2017)
Katarzyna Świderek, Iñaki Tuñón, Vicent Moliner, Joan Bertran
Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3. Chemistry (Weinheim an der Bergstrasse, Germany) 23 (31) (2017)
Kirill Zinovjev, Iñaki Tuñón
Adaptive Finite Temperature String Method in Collective Variables. The journal of physical chemistry. A 121 (51) (2017)
Juan Aranda, Antonio Francés-Monerris, Iñaki Tuñón, Daniel Roca-Sanjuán
Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations. Journal of chemical theory and computation 13 (10) (2017)
Jose Javier Ruiz-Pernía, Enas Behiry, Louis Y P Luk, Edric Joel Loveridge, Iñaki Tuñón, Vicent Moliner, Rudolf K Allemann
Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chemical science 7 (5) (2016)