Alexander V Nemukhin

Affiliations

Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation. khrenova.maria@gmail.com wasabiko@lcc.chem.msu.ru and Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russian Federation.

ORCID: 0000-0002-4992-6029

Publications (29)

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRAS

Organic & biomolecular chemistry

Avec: Maria G Khrenova , Anna M Kulakova , Alexander V Nemukhin

[Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1].

Biomeditsinskaia khimiia

Avec: A M Kulakova , M G Khrenova , A V Nemukhin

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur.

Journal of chemical theory and computation

Avec: Goran Giudetti , Igor Polyakov , Bella L Grigorenko , Shirin Faraji , Alexander V Nemukhin , Anna I Krylov

Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors.

Physical chemistry chemical physics : PCCP

Avec: Maria G Khrenova , Vladimir G Tsirelson , Alexander V Nemukhin

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling.

Organic & biomolecular chemistry

Avec: Bella L Grigorenko , Ekaterina D Kots , Alexander V Nemukhin

Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase.

Journal of chemical information and modeling

Avec: Maria G Khrenova , Anna M Kulakova , Alexander V Nemukhin

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase.

Molecules (Basel, Switzerland)

Avec: Alexandra V Krivitskaya , Maria G Khrenova , Alexander V Nemukhin

Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation.

Journal of chemical information and modeling

Avec: Maria G Khrenova , Fedor D Mulashkin , Alexander V Nemukhin

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms.

Journal of the American Chemical Society

Avec: Bella L Grigorenko , Igor V Polyakov , Maria G Khrenova , Goran Giudetti , Shirin Faraji , Anna I Krylov , Alexander V Nemukhin

Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang.

The journal of physical chemistry. B

Avec: Bella L Grigorenko , Igor V Polyakov , Anna I Krylov , Alexander V Nemukhin

Novel flavin-based fluorescent proteins with red-shifted emission bands: a computational study.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology

Avec: Yulia I Meteleshko , Alexander V Nemukhin , Maria G Khrenova

Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase.

Journal of chemical information and modeling

Avec: Ekaterina D Kots , Maria G Khrenova , Alexander V Nemukhin

Structure of the Brain

ACS chemical neuroscience

Avec: Igor V Polyakov , Artem E Kniga , Bella L Grigorenko , Alexander V Nemukhin

Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step.

Chemical science

Avec: Husam Sabah Auhim , Bella L Grigorenko , Tessa K Harris , Ozan E Aksakal , Igor V Polyakov , Colin Berry , Gabriel Dos Passos Gomes , Igor V Alabugin , Pierre J Rizkallah , Alexander V Nemukhin , D Dafydd Jones

Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins.

Organic & biomolecular chemistry

Avec: Bella L Grigorenko , Maria G Khrenova , D Dafydd Jones , Alexander V Nemukhin

Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang.

Molecules (Basel, Switzerland)

Avec: Bella L Grigorenko , Igor V Polyakov , Alexander V Nemukhin

Computer-designed active human butyrylcholinesterase double mutant with a new catalytic triad.

Chemico-biological interactions

Avec: Bella L Grigorenko , Dana A Novichkova , Sofya V Lushchekina , Irina V Zueva , Lawrence M Schopfer , Alexander V Nemukhin , Sergey D Varfolomeev , Oksana Lockridge , Patrick Masson

Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang.

The journal of physical chemistry. B

Avec: Tirthendu Sen , Yingying Ma , Igor V Polyakov , Bella L Grigorenko , Alexander V Nemukhin , Anna I Krylov

Computer Modeling of N-Acetylglutamate Synthase: From Primary Structure to Elemental Stages of Catalysis.

Doklady. Biochemistry and biophysics

Avec: I V Polyakov , A E Kniga , B L Grigorenko , A V Nemukhin , S D Varfolomeev

[In silico specificity determination of neoantigen-reactive T-lymphocytes].

Biomeditsinskaia khimiia

Avec: A E Kniga , I V Polyakov , A V Nemukhin

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices.

Angewandte Chemie (Weinheim an der Bergstrasse, Germany)

Avec: Xinzhao Xu , Benjamin J Bowen , Rebecca E A Gwyther , Mark Freeley , Bella Grigorenko , Alexander V Nemukhin , Johnas Eklöf-Österberg , Kasper Moth-Poulsen , D Dafydd Jones , Matteo Palma

Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen.

Molecular informatics

Avec: Igor V Polyakov , Alexander V Nemukhin , Tatiana M Domratcheva , Anna M Kulakova , Bella L Grigorenko

Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes.

The journal of physical chemistry. B

Avec: Alexander V Nemukhin , Bella L Grigorenko , Maria G Khrenova , Anna I Krylov

Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2.

The journal of physical chemistry letters

Avec: Bella L Grigorenko , Tatiana Domratcheva , Igor V Polyakov , Alexander V Nemukhin

Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores.

Journal of chemical information and modeling

Avec: Maria G Khrenova , Fedor D Mulashkin , Egor S Bulavko , Tatiana M Zakharova , Alexander V Nemukhin

Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4.

The Journal of chemical physics

Avec: Bella L Grigorenko , Igor V Polyakov , Alexander V Nemukhin

Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2.

Russian chemical bulletin = Izvestiia Akademii nauk. Seriia khimicheskaia

Avec: A V Nemukhin , B L Grigorenko , S V Lushchekina , S D Varfolomeev

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices.

Angewandte Chemie (International ed. in English)

Avec: Xinzhao Xu , Benjamin J Bowen , Rebecca E A Gwyther , Mark Freeley , Bella Grigorenko , Alexander V Nemukhin , Johnas Eklöf-Österberg , Kasper Moth-Poulsen , D Dafydd Jones , Matteo Palma

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials.

Molecules (Basel, Switzerland)

Avec: Maria G Khrenova , Egor S Bulavko , Fedor D Mulashkin , Alexander V Nemukhin

Réseau de co-auteurs

Bella L Grigorenko 14 collaborations

Maria G Khrenova 12 collaborations

Igor V Polyakov 9 collaborations

Anna I Krylov 5 collaborations

A V Nemukhin 4 collaborations

D Dafydd Jones 4 collaborations

Anna M Kulakova 3 collaborations

Fedor D Mulashkin 3 collaborations

Goran Giudetti 2 collaborations

Shirin Faraji 2 collaborations

Ekaterina D Kots 2 collaborations

I V Polyakov 2 collaborations

A E Kniga 2 collaborations

B L Grigorenko 2 collaborations

S D Varfolomeev 2 collaborations

Xinzhao Xu 2 collaborations

Benjamin J Bowen 2 collaborations

Rebecca E A Gwyther 2 collaborations

Mark Freeley 2 collaborations

Bella Grigorenko 2 collaborations

Johnas Eklöf-Österberg 2 collaborations

Kasper Moth-Poulsen 2 collaborations

Matteo Palma 2 collaborations

Egor S Bulavko 2 collaborations

A M Kulakova 1 collaboration

M G Khrenova 1 collaboration

Igor Polyakov 1 collaboration

Vladimir G Tsirelson 1 collaboration

Alexandra V Krivitskaya 1 collaboration

Yulia I Meteleshko 1 collaboration

Artem E Kniga 1 collaboration

Husam Sabah Auhim 1 collaboration

Tessa K Harris 1 collaboration

Ozan E Aksakal 1 collaboration

Colin Berry 1 collaboration

Gabriel Dos Passos Gomes 1 collaboration

Igor V Alabugin 1 collaboration

Pierre J Rizkallah 1 collaboration

Dana A Novichkova 1 collaboration

Sofya V Lushchekina 1 collaboration

Irina V Zueva 1 collaboration

Lawrence M Schopfer 1 collaboration

Sergey D Varfolomeev 1 collaboration

Oksana Lockridge 1 collaboration

Patrick Masson 1 collaboration

Tirthendu Sen 1 collaboration

Yingying Ma 1 collaboration

Tatiana M Domratcheva 1 collaboration

Tatiana Domratcheva 1 collaboration

Tatiana M Zakharova 1 collaboration

S V Lushchekina 1 collaboration