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J

J. Javier Ruiz‐Pernía

universitat de valencia

26H-index
99Paper Count
1.9KCitation Count
Published Papers 44
Publication Date
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Protonation and magnesium ions shape the transition state diversity of phosphoanhydride hydrolysis in water
errNature Communications
IF15.7
err2026-05-27
err0
errOAAI
errAdrián García-Martínez; Miguel de la Puente; Marion Cunin; Kirill Zinovjev; J. Javier Ruiz-Pernía; Damien Laage; Iñaki Tuñón
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Adapted DFTB3 Repulsive Potentials Reach DFT Accuracy for Hydride Transfer Reactions in Enzymes
errJournal of Computational Chemistry
IF4.8
err2025-07-14
err0
PREAI
errJosé Luís Velázquez-Libera; Rodrigo Recabarren; David Adrian Saez; Carlos Castillo; J. Javier Ruiz-Pernía; Iñaki Tuñón; Esteban Vöhringer-Martinez
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Multiobjective Evolutionary Strategy for Improving Semiempirical Hamiltonians in the Study of Enzymatic Reactions at the QM/MM Level of Theory
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2025-05-07
err0
PREAI
errVelazquez-Libera, Jose Luis; Recabarren, Rodrigo; Vohringer-Martinez, Esteban; Salgueiro, Yamisleydi; Ruiz-Pernia, J. Javier; Caballero, Julio
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Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l-Asparaginase Type 1 for Leukemia Drug Design
errACS CATALYSIS
IF13.1
err2025-04-29
err0
PREAI
errAndjelkovic, M; Zinovjev, K; Ruiz-Pernía, JJ; Tunón, I
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errSave
Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2025-03-28
err0
PREAI
errGarcia-Meseguer, Rafael; Duboue-Dijon, Elise; Marti, Sergio; Ruiz-Pernia, J. Javier; Laage, Damien; Tunon, Inaki; Hynes, James T.
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Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism
errACS CATALYSIS
IF13.1
err2025-02-27
err0
PREAI
errPardos, J; García-Martínez, A; Ruiz-Pernía, JJ; Tuñón, I
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Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease: Implications for Resistance Mechanisms from Computations
errANGEWANDTE CHEMIE-INTERNATIONAL EDITION
IF16.9
err2024-09-02
err0
errOAAI
errSchillings, Johanna; Ramos-Guzman, Carlos A.; Ruiz-Pernia, J. Javier; Tunon, Inaki
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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
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-05-04
err1
PREAI
errVelazquez-Libera, Jose Luis; Caballero, Julio; Alzate-Morales, Jans; Ruiz-Pernia, J. Javier; Tunon, Inaki
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errSave
Activation and friction in enzymatic loop opening and closing dynamics
errNATURE COMMUNICATIONS
IF15.7
err2024-03-20
err2
errOAAI
errZinovjev, Kirill; Guenon, Paul; Ramos-Guzman, Carlos A.; Ruiz-Pernia, J. Javier; Laage, Damien; Tunon, Inaki
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errSave
Electrostatics as a Guiding Principle in Understanding and Designing Enzymes
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-02-27
err8
errOAAI
errRuiz-Pernia, J. Javier; Swiderek, Katarzyna; Bertran, Joan; Moliner, Vicent; Tunon, Inaki
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errSave
Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2023-11-03
err2
errOAAI
errGarcia-Martinez, Adrian; Zinovjev, Kirill; Ruiz-Pernia, Jose Javier; Tunon, Inaki
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errSave
Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2023-08-16
err22
errOAAI
errGarcia-Meseguer, Rafael; Orti, Enrique; Tunon, Inaki; Ruiz-Pernia, J. Javier; Arago, Juan
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errSave
Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations.
errCHEMCATCHEM
IF3.9
err2023-07-04
err3
PREAI
errVelazquez-Libera, Jose Luis; Caballero, Julio; Alzate-Morales, Jans; Ruiz-Pernia, J. Javier; Tunon, Inaki
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errSave
Unveiling the Mechanist i c Singulariti e s of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1
errACS CATALYSIS
IF13.1
err2023-03-15
err1
errOAAI
errRamos-Guzman, Carlos A. .; Ruiz-Pernia, J. Javier; Zinovjev, Kirill; Tunon, Inaki
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errSave
The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms
errCHEMICAL SCIENCE
IF7.4
err2023-01-01
err15
errOAAI
errRamos-Guzman, Carlos A.; Andjelkovic, Milorad; Zinovjev, Kirill; Ruiz-Pernia, J. Javier; Tunon, Inaki
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Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-05-13
err14
errOAAI
errRamos-Guzman, Carlos A.; Luis Velazquez-Libera, Jose; Javier Ruiz-Pernia, J.; Tunon, Inaki
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errSave
Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations (vol 701, 108807, 2021)
errARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
IF3
err2021-08-01
err0
PREAI
errAlvarado, Omar; Garcia-Meseguer, Rafael; Ruiz-Pernia, Jose Javier; Tunon, Inaki; Delgado, Eduardo J.
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errSave
Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations
errARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
IF3
err2021-08-01
err0
PREAI
errAlvarado, Omar; Garcia-Meseguer, Rafael; Ruiz-Pernia, Jose Javier; Tunon, Inaki; Delgado, Eduardo J.
errShare
errSave
Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations
errARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
IF3
err2021-04-01
err3
PREAI
errAlvarado, Omar; Garcia-Meseguer, Rafael; Javier Ruiz-Pernia, Jose; Tunon, Inaki; Delgado, Eduardo J.
errShare
errSave
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism
errACS CATALYSIS
IF13.1
err2021-03-25
err42
PREAI
errRamos-Guzman, Carlos A.; Javier Ruiz-Pernia, J.; Tunon, Inaki
errShare
errSave

Research Directions

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Co-authors
Cooperation Journals
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H-index: 97 · Papers: 423
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Jiali Gao
H-index: 82 · Papers: 428
C
Carlos Fernández‐del Castillo
H-index: 81 · Papers: 733
A
Adrian J. Mulholland
H-index: 71 · Papers: 474
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