Article-Journal

Electrostatic Embedding of Machine Learning Potentials
This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials …
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Electrostatic Embedding of Machine Learning Potentials
The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms
The use of antiviral drugs can promote the appearance of mutations in the target protein that increase the resistance of the virus to …
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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
Cysteine proteases are an important target for the development of inhibitors that could be used as drugs to regulate the activity of …
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Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs
We present the results of classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a hydroxymethylketone …
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Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease
We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed …
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Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations
In this work, we studied the biosynthesis of R-phenylacetylcarbinol (R-PAC) by acetohydroxy acid synthase (AHAS) using molecular …
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Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism
We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those …
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A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design
The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor known as N3 has been investigated using multiscale …
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Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods
We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using …
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On the Nature of the Enzyme - Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study
In this work, we conducted a comprehensive theoretical analysis of l-arginine hydrolysis catalyzed by human arginase I (HARGI). We …
Jose Luis Velázquez , J. Caballero , Iñaki Tuñón , E.W. Hernandez-Rodriguez , J. Javier Ruiz-Pernía
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On the Nature of the Enzyme - Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study