Publications

Felipe Bravo Moraga , Mauricio Bedoya , Kirill Zinovjev , Iñaki Tuñón , Jans Alzate-Morales (2025). Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations. ACS Omega.

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Rafael García Meseguer , Elise Duboué-Dijon , Sergio Martí , J. Javier Ruiz-Pernía , Damien Laage , Iñaki Tuñón , James T. Hynes (2025). Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity. J. Chem. Phys..

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Jorge Pardos , Adrián García-Martínez , J. Javier Ruiz-Pernía , Iñaki Tuñón (2025). Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism. ACS Catal..

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Rafael García-Meseguer , Miriam Navarrete-Miguel , Sergio Martí , Iñaki Tuñón , Daniel Roca-Sanjuán (2025). DNA Triplet Energies by Free Energy Perturbation Theory. J. Chem. Theory Comput..

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Katarzyna Świderek , Joan Bertran , Kirill Zinovjev , Iñaki Tuñón , Vicent Moliner (2025). Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age. WIREs Comput. Mol. Sci..

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Janko Civic , Iñaki Tuñón , Jeremy N. Harvey (2025). Understanding Substrate Binding and Reactivity of Stearoyl-CoA Desaturase (SCD1) through Classical and Multiscale Molecular Dynamics Simulations. J. Chem. Theory. Comput..

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Kirill Zinovjev , Carles Curutchet (2025). Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials. J. Phys. Chem. Lett..

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Milorad Andjelkovic , Kirill Zinovjev , J. Javier Ruiz-Pernía , Iñaki Tuñón (2024). Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig L-Asparaginase Type 1 for Leukemia Drug Design. ChemRxiv.

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Johanna Schillings , Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2024). Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease: Implications for Resistance Mechanisms from Computations. Angew. Chem. Int. Ed..

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Kirill Zinovjev , Lester Hedges , Rubén Montagud Andreu , Christopher Woods , Iñaki Tuñón , Marc W. Van Der Kamp (2024). emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. J. Chem. Theory. Comput..

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Rolf David , Iñaki Tuñón , Damien Laage (2024). Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J. Am. Chem. Soc..

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Jose Luis Velázquez , J. Caballero , J. Alzate-Morales , J. Javier Ruiz-Pernía , Iñaki Tuñón (2024). 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.

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Kirill Zinovjev , Paul Guénon , Carlos Ramos , J. Javier Ruiz-Pernía , Damien Laage , Iñaki Tuñón (2024). Activation and friction in enzymatic loop opening and closing dynamics. Nat. Commun..

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J. Javier Ruiz-Pernía , K. Swiderek , J. Bertran , V. Moliner , Iñaki Tuñón (2024). Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J. Chem. Theory. Comput..

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Milorad Andjelkovic , Kirill Zinovjev , Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2023). Elucidation of the active form and reaction mechanism in human asparaginase type III using multiscale simulations. J. Chem. Inf. Model..

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Adrián García-Martínez , Kirill Zinovjev , J. Javier Ruiz-Pernía , Iñaki Tuñón (2023). Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations. J. Am. Chem. Soc..

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Rafael García Meseguer , E. Orti , Iñaki Tuñón , J. Javier Ruiz-Pernía , J. Arago (2023). Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling. Journal of the American Chemical Society.

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Jose Luis Velázquez , J. Caballero , J. Alzate-Morales , J. Javier Ruiz-Pernía , Iñaki Tuñón (2023). Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations. ChemCatChem.

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Carlos Ramos , J. Javier Ruiz-Pernía , Kirill Zinovjev , Iñaki Tuñón (2023). Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1. ACS Catal..

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Kirill Zinovjev (2023). Electrostatic Embedding of Machine Learning Potentials. J. Chem. Theory. Comput..

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Carlos Ramos , Milorad Andjelkovic , Kirill Zinovjev , J. Javier Ruiz-Pernía , Iñaki Tuñón (2023). The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms. Chem. Sci..

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón , Jose Luis Velázquez (2022). Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition. J. Chem. Theory Comput..

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2021). Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs. Angew. Chem. Int. Ed..

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2021). Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease. Chem. Commun..

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O. Alvarado , Rafael García Meseguer , J. Javier Ruiz-Pernía , Iñaki Tuñón , E.J. Delgado (2021). Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Archives of Biochemistry and Biophysics.

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2021). Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism. ACS Catal..

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2021). A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design. Chem. Sci..

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Carlos Ramos , J. Javier Ruiz-Pernía , Iñaki Tuñón (2020). Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods. ACS Catal..

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Jose Luis Velázquez , J. Caballero , Iñaki Tuñón , E.W. Hernandez-Rodriguez , J. Javier Ruiz-Pernía (2020). On the Nature of the Enzyme - Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study. ACS Catalysis.

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A. Angelastro , J. Javier Ruiz-Pernía , Iñaki Tuñón , V. Moliner , L.Y.P. Luk , R.K. Allemann (2019). Loss of Hyperconjugative Effects Drives Hydride Transfer during Dihydrofolate Reductase Catalysis. ACS Catalysis.

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J. Javier Ruiz-Pernía , Iñaki Tuñón , V. Moliner , R.K. Allemann (2019). Why are some enzymes dimers? Flexibility and catalysis in thermotoga maritima dihydrofolate reductase. ACS Catalysis.

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J. Navarro-Sanchez , N. Almora-Barrios , B. Lerma-Berlanga , J. Javier Ruiz-Pernía , V.A. Lorenz-Fonfria , Iñaki Tuñón , C. Marti-Gastaldo (2019). Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions. Chemical Science.

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O. Alvarado , Rafael García Meseguer , J. Javier Ruiz-Pernía , Iñaki Tuñón , E.J. Delgado (2019). A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS. Chemical Physics Letters.

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Maite Roca , J. Javier Ruiz-Pernía , R. Castillo , M. Oliva , V. Moliner (2018). Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase. Physical Chemistry Chemical Physics.

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E. M. Behiry , J. Javier Ruiz-Pernía , L.Y.P Luk , Iñaki Tuñón , V. Moliner , R.K. Allemann (2018). Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State. Angewandte Chemie - International Edition.

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Carlos Ramos , Kirill Zinovjev , Iñaki Tuñón (2018). Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design. Eur. J. Med. Chem..

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Kirill Zinovjev , Iñaki Tuñón (2017). Adaptive Finite Temperature String Method in Collective Variables.

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N. Guillet , J. Javier Ruiz-Pernía , A. De La Lande , B. Levy , F. Lederer , I. Demachy , V. Moliner (2016). QM/MM study of l-lactate oxidation by flavocytochrome: B2. Physical Chemistry Chemical Physics.

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J. Javier Ruiz-Pernía , E. Behiry , L.Y.P. Luk , E.J. Loveridge , Iñaki Tuñón , V. Moliner , R.K Allemann (2016). Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chemical Science.

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I. Sánchez-Moreno , I. Bordes , R. Castillo , J. Javier Ruiz-Pernía , V. Moliner , E. García-Junceda (2015). Tuning the phosphoryl donor specificity of dihydroxyacetone kinase from ATP to inorganic polyphosphate. An insight from computational studies. International Journal of Molecular Sciences.

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J. Javier Ruiz-Pernía , V. Moliner , Iñaki Tuñón (2015). Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase. Quantum Modeling of Complex Molecular Systems.

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I. Bordes , J. Javier Ruiz-Pernía , R. Castillo , V. Moliner (2015). A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution. Organic and Biomolecular Chemistry.

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L.Y.P. Louis , J. Javier Ruiz-Pernía , A.S. Adesina , E.J. Loveridge , Iñaki Tuñón , V. Moliner , R.K. Allemann (2015). Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angewandte Chemie - International Edition.

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