Unraveling the SARS-CoV‑2 Main Protease Mechanism Using Multiscale Methods
Ramos-Guzmán, Carlos A, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
Published in ACS catalysis (06.11.2020)
Published in ACS catalysis (06.11.2020)
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Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs
Ramos‐Guzmán, Carlos A., Ruiz‐Pernía, J. Javier, Tuñón, Iñaki
Published in Angewandte Chemie International Edition (01.12.2021)
Published in Angewandte Chemie International Edition (01.12.2021)
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Multiscale Simulations of SARS-CoV‑2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism
Ramos-Guzmán, Carlos A, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
Published in ACS catalysis (02.04.2021)
Published in ACS catalysis (02.04.2021)
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Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
Luk, Louis Y. P., Ruiz-Pernía, J. Javier, Dawson, William M., Roca, Maite, Loveridge, E. Joel, Glowacki, David R., Harvey, Jeremy N., Mulholland, Adrian J., Tuñón, Iñaki, Moliner, Vicent, Allemann, Rudolf K.
Published in Proceedings of the National Academy of Sciences - PNAS (08.10.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (08.10.2013)
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Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS‐CoV‐2 Main Protease: Implications for Resistance Mechanisms from Computations
Schillings, Johanna, Ramos‐Guzmán, Carlos A., Ruiz‐Pernía, J. Javier, Tuñón, Iñaki
Published in Angewandte Chemie International Edition (01.10.2024)
Published in Angewandte Chemie International Edition (01.10.2024)
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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
Velázquez-Libera, José Luis, Caballero, Julio, Alzate-Morales, Jans, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
Published in Journal of chemical information and modeling (27.05.2024)
Published in Journal of chemical information and modeling (27.05.2024)
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Journal Article
Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV‑2 3CL Protease Inhibition
Ramos-Guzmán, Carlos A., Velázquez-Libera, José Luis, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
Published in Journal of chemical theory and computation (14.06.2022)
Published in Journal of chemical theory and computation (14.06.2022)
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Why Are Some Enzymes Dimers? Flexibility and Catalysis in Thermotoga maritima Dihydrofolate Reductase
Ruiz-Pernía, J. Javier, Tuñón, Iñaki, Moliner, Vicent, Allemann, Rudolf K
Published in ACS catalysis (05.07.2019)
Published in ACS catalysis (05.07.2019)
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Heavy enzymes—experimental and computational insights in enzyme dynamics
Świderek, Katarzyna, Javier Ruiz-Pernía, J, Moliner, Vicent, Tuñón, Iñaki
Published in Current opinion in chemical biology (01.08.2014)
Published in Current opinion in chemical biology (01.08.2014)
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Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations
Velázquez‐Libera, José Luis, Caballero, Julio, Alzate‐Morales, Jans, Ruiz‐Pernía, J. Javier, Tuñón, Iñaki
Published in ChemCatChem (08.09.2023)
Published in ChemCatChem (08.09.2023)
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Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O‑Methyltransferase
García-Meseguer, Rafael, Zinovjev, Kirill, Roca, Maite, Ruiz-Pernía, Javier J, Tuñón, Iñaki
Published in The journal of physical chemistry. B (22.01.2015)
Published in The journal of physical chemistry. B (22.01.2015)
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Journal Article
Protein Isotope Effects in Dihydrofolate Reductase From Geobacillus stearothermophilus Show Entropic–Enthalpic Compensatory Effects on the Rate Constant
Luk, Louis Y. P., Ruiz-Pernía, J. Javier, Dawson, William M., Loveridge, E. Joel, Tuñón, Iñaki, Moliner, Vicent, Allemann, Rudolf K.
Published in Journal of the American Chemical Society (10.12.2014)
Published in Journal of the American Chemical Society (10.12.2014)
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A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design
Ramos-Guzmán, Carlos A, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
Published in Chemical Science (18.03.2021)
Published in Chemical Science (18.03.2021)
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Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions
Navarro, Jose, Almora Barrios, Neyvis, Lerma Berlanga, Belén, Ruiz-Pernía, J. Javier, Lorenz Fonfria, Victor Armando, Tuñón, Iñaki, Martí-Gastaldo, Carlos
Published in Chemical science (Cambridge) (14.04.2019)
Published in Chemical science (Cambridge) (14.04.2019)
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