Article-Journal

Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l-Asparaginase Type 1 for Leukemia Drug Design
In this study, we present a computational analysis of the catalytic properties of guinea pig asparaginase type 1 (or gpASNase1), an …
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Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l-Asparaginase Type 1 for Leukemia Drug Design
Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations
Residence time is a crucial parameter for assessing the functional efficacy of drugs, quantifying the duration of a drug’s binding to …
Felipe Bravo Moraga , Mauricio Bedoya , Kirill Zinovjev , Iñaki Tuñón , Jans Alzate-Morales
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Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations
Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity
It is now well established that the transition state of a chemical reaction is not a single, static structure but rather a distribution …
Rafael García Meseguer , Elise Duboué-Dijon , Sergio Martí , J. Javier Ruiz-Pernía , Damien Laage , Iñaki Tuñón , James T. Hynes
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Molecular dynamics simulations for enzymatic hydride-transfer reactions: Defining environmental reaction coordinates to capture transition state diversity
Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism
We present a systematic evaluation of different possible reaction mechanisms for GTP hydrolysis in RhoA, a member of the Ras …
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Mechanistic Insights into GTP Hydrolysis by the RhoA Protein: Catalytic Impact of Glutamine Tautomerism
DNA Triplet Energies by Free Energy Perturbation Theory
Determining the energetics of triplet electronic states of nucleobases in the biological macromolecular environment of nucleic acids is …
Rafael García-Meseguer , Miriam Navarrete-Miguel , Sergio Martí , Iñaki Tuñón , Daniel Roca-Sanjuán
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DNA Triplet Energies by Free Energy Perturbation Theory
Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age
The study of natural enzyme catalytic processes at a molecular level can provide essential information for a rational design of new …
Katarzyna Świderek , Joan Bertran , Kirill Zinovjev , Iñaki Tuñón , Vicent Moliner
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Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age
Understanding Substrate Binding and Reactivity of Stearoyl-CoA Desaturase (SCD1) through Classical and Multiscale Molecular Dynamics Simulations
Stearoyl-CoA desaturase (SCD1) plays an important role in the metabolism of fatty acids and is a promising therapeutic target. However, …
Janko Civic , Iñaki Tuñón , Jeremy N. Harvey
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Understanding Substrate Binding and Reactivity of Stearoyl-CoA Desaturase (SCD1) through Classical and Multiscale Molecular Dynamics Simulations
Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials
Incorporation of environment and vibronic effects in simulations of optical spectra and excited state dynamics is commonly done by …
Kirill Zinovjev , Carles Curutchet
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Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials
Pomotrelvir and Nirmatrelvir Binding and Reactivity with SARS-CoV-2 Main Protease: Implications for Resistance Mechanisms from Computations
We investigate the inhibition mechanism between pomotrelvir and the SARS-CoV-2 main protease using molecular mechanics and quantum …
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emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations
We present in this work the emle-engine package (https://github.com/chemle/emle-engine)─the implementation of a new machine learning …
Kirill Zinovjev , Lester Hedges , Rubén Montagud Andreu , Christopher Woods , Iñaki Tuñón , Marc W. Van Der Kamp
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emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations