List of works - José Javier Ruiz-Pernía

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition

scientific article published on 10 April 2012

A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

scientific article published on 01 July 2005

A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution.

scientific article published on 25 August 2015

Activation Free Energy of CatecholO-Methyltransferase. Corrections to the Potential of Mean Force†

scientific article published in January 2006

Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study

scientific article published on 29 February 2008

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase

scientific article

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction

scientific article published on 01 October 2006

Computational simulation of the lifetime of the methoxymethyl cation in water. A simple model for a glycosyl cation: when is an intermediate an intermediate?

scientific article published in May 2010

Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.

scientific article published on February 2009

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach.

scientific article published on 14 May 2008

Ensemble-averaged QM/MM kinetic isotope effects for the S(N)2 reaction of cyanide anions with chloroethane in DMSO solution

scientific article published on 26 June 2012

Enzymatic effects on reactant and transition states. The case of chalcone isomerase

scientific article published on 28 June 2007

Heavy enzymes--experimental and computational insights in enzyme dynamics

scientific article published on 05 April 2014

Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes

scientific article published on 01 September 2006

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

scientific article published on January 2011

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

scientific article published on 28 June 2012

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

scientific article published on 26 November 2013

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

scientific article published on 17 January 2018

Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase

scientific article published on 10 September 2014

Minimization of dynamic effects in the evolution of dihydrofolate reductase† †Electronic supplementary information (ESI) available: Full experimental procedures; mass spectra of purified proteins; circular dichroism spectra, tabulated experimental d

scientific article published on 3 February 2016

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant

scientific article published on 26 November 2014

QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects

scientific article published on 29 October 2008

QM/MM study of l-lactate oxidation by flavocytochrome b2.

scientific article published on 25 May 2016

Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

scientific article published on 13 May 2022

Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

scientific article published on March 2009

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

scientific article published on 5 July 2013

Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions

scientific article published on 28 February 2019

Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies

scientific article published on 24 November 2015

Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase

scientific article published on 13 May 2019

List of works by José Javier Ruiz-Pernía