Jose J. Pernia-Ruiz

Burjassot, VC, Spain

Last Updated: 09/26/2026

Save publications for later

Sign Up

Not sure about your diagnosis?

Check Your Symptoms

Found 35 publications

Protonation and magnesium ions shape the transition state diversity of phosphoanhydride hydrolysis in water.

Protonation and magnesium ions shape the transition state diversity of phosphoanhydride hydrolysis in water.

Journal: Nature communications

Published: December 10, 2025

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

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

Journal: Journal of chemical theory and computation

Published: May 07, 2025

Adapted DFTB3 Repulsive Potentials Reach DFT Accuracy for Hydride Transfer Reactions in Enzymes.

Adapted DFTB3 Repulsive Potentials Reach DFT Accuracy for Hydride Transfer Reactions in Enzymes.

Journal: Journal of computational chemistry

Published: March 18, 2025

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

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

Journal: ACS catalysis

Published: January 27, 2025

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

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

Journal: The Journal of chemical physics

Published: December 21, 2024

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

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

Journal: ACS catalysis

Published: December 17, 2024

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

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

Journal: Angewandte Chemie (International ed. in English)

Published: May 25, 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.

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: Journal of chemical information and modeling

Published: May 04, 2024

Electrostatics as a Guiding Principle in Understanding and Designing Enzymes.

Electrostatics as a Guiding Principle in Understanding and Designing Enzymes.

Journal: Journal of chemical theory and computation

Published: February 27, 2024

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

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

Journal: Journal of chemical information and modeling

Published: August 28, 2023

Activation and friction in enzymatic loop opening and closing dynamics.

Activation and friction in enzymatic loop opening and closing dynamics.

Journal: Nature communications

Published: August 02, 2023

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

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

Journal: ACS catalysis

Published: January 03, 2023

Showing 1-12 of 35

Last Updated: 09/26/2026