Publikationen, an denen er mitarbeitet JOSE JAVIER RUIZ PERNIA (53)

2024

  1. Activation and friction in enzymatic loop opening and closing dynamics

    Nature Communications, Vol. 15, Núm. 1

  2. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

    Journal of Chemical Theory and Computation, Vol. 20, Núm. 5, pp. 1783-1795

  3. Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease: Implications for Resistance Mechanisms from Computations

    Angewandte Chemie - International Edition, Vol. 63, Núm. 40

2023

  1. 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, Vol. 145, Núm. 45, pp. 24809-24819

  2. Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations

    Journal of Chemical Information and Modeling, Vol. 63, Núm. 17, pp. 5676-5688

  3. Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling

    Journal of the American Chemical Society, Vol. 145, Núm. 35, pp. 19243-19255

  4. Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations.

    ChemCatChem, Vol. 15, Núm. 17

  5. MM and QMMM trayectories from "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations"

    Zenodo

  6. MM and QMMM trayectories from "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations"

    Zenodo

  7. The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms

    Chemical Science, Vol. 14, Núm. 10, pp. 2686-2697

  8. 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

  9. Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1

    ACS Catalysis, Vol. 13, Núm. 7, pp. 4348-4361

2022

  1. 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, Vol. 18, Núm. 6, pp. 4005-4013

2021

  1. A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design

    Chemical Science, Vol. 12, Núm. 10, pp. 3489-3496

  2. Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease

    Chemical Communications, Vol. 57, Núm. 72, pp. 9096-9099

  3. Corrigendum to “Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations” [Arch. Biochem. Biophys. 701 (2021) 108807] (Arch. Biochem. Biophys.(2021) 701 (108807) (S0003-9861(21)00057-6) (10.1016/j.abb.2021.108807))

    Archives of Biochemistry and Biophysics

  4. Erratum: Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations (Archives of Biochemistry and Biophysics (2021) 701, (S0003986121000576), (10.1016/j.abb.2021.108807))

    Archives of Biochemistry and Biophysics

  5. Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**

    Angewandte Chemie - International Edition, Vol. 60, Núm. 49, pp. 25933-25941

  6. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations

    Archives of Biochemistry and Biophysics, Vol. 701

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

    ACS Catalysis, Vol. 11, Núm. 7, pp. 4157-4168