Publications (64) JOSE JAVIER RUIZ PERNIA publications View referenced research data.

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2025

  1. Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism

    ACS Catalysis, Vol. 15, Núm. 6, pp. 4415-4428

  2. Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity

    Journal of Chemical Physics, Vol. 162, Núm. 12

  3. Multiobjective Evolutionary Strategy for Improving Semiempirical Hamiltonians in the Study of Enzymatic Reactions at the QM/MM Level of Theory

    Journal of Chemical Theory and Computation, Vol. 21, Núm. 10, pp. 5118-5131

  4. Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l-Asparaginase Type 1 for Leukemia Drug Design

    ACS Catalysis, Vol. 15, Núm. 10, pp. 7919-7933

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

  4. 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, Vol. 64, Núm. 10, pp. 4134-4148

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. 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

  6. 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