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Biological and Medicinal Chemistry

Working Paper

Enlighten2: Molecular Dynamics Simulations of Protein-Ligand Systems Made Accessible

Kirill Zinovjev, Marc W. van der Kamp

Version 2 posted 16 June 2020

2,260

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Theoretical and Computational Chemistry

Working Paper

Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

Adrián García-Martínez, Kirill Zinovjev, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 02 August 2023

144

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Theoretical and Computational Chemistry

Working Paper

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, Iñaki Tuñón, Marc W. van der Kamp

Version 2 posted 27 February 2024

682

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Biological and Medicinal Chemistry

Working Paper

Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatases

Kirill Zinovjev, Paul Guénon, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón

Version 1 posted 03 July 2023

344

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Theoretical and Computational Chemistry

Working Paper

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

Rodrigo Recabarren, Kirill Zinovjev, Iñaki Tuñón, Jans Alzate-Morales

Version 1 posted 01 July 2020

881

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Theoretical and Computational Chemistry

Working Paper

Catalytic Reaction Mechanism in Native and Mutant COMT from the Adaptive String Method and Mean Reaction Force Analysis.

David Adrian Saez, Kirill Zinovjev, Iñaki Tuñon, Esteban Vöhringer-Martinez

Version 1 posted 10 May 2018

549

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Biological and Medicinal Chemistry

Working Paper

Virtual reality sampled pathways guide free energy calculation of protein-ligand binding

Helen Deeks, Kirill Zinovjev, Jonathan Barnoud, Adrian Mulholland, Marc van der Kamp, David Glowacki

Version 1 posted 19 April 2022

364

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Theoretical and Computational Chemistry

Working Paper

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

Carlos A. Ramos-Guzmán, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 23 November 2022

253

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Theoretical and Computational Chemistry

Working Paper

Electrostatic Embedding of Machine Learning Potentials

Kirill Zinovjev

Version 3 posted 07 September 2022

611

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Improved description of environment and vibronic effects with electrostatically embedded ML potentials

Kirill Zinovjev, Carles Curutchet

Version 1 posted 09 October 2024

93

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10 results in Kirill Zinovjev in Authors: Kirill Zinovjev

Enlighten2: Molecular Dynamics Simulations of Protein-Ligand Systems Made Accessible

Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations

Loop opening and closing dynamics in enzymes: activated or friction-limited? The case of protein tyrosine phosphatases

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

Catalytic Reaction Mechanism in Native and Mutant COMT from the Adaptive String Method and Mean Reaction Force Analysis.

Virtual reality sampled pathways guide free energy calculation of protein-ligand binding

Impact of SARS-CoV-2 3CL Protease Mutations on Nirmatrelvir Inhibitory Efficiency. Computational Insights into Potential Resistance Mechanisms

Electrostatic Embedding of Machine Learning Potentials

Improved description of environment and vibronic effects with electrostatically embedded ML potentials

10 results in Authors: Kirill Zinovjev