Alexander V Nemukhin (Alexander Nemukhin)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 34

Top Topics

Protein Protein

Molecular Dynamics

Top Venues

Molecules (Basel, Switzerland)

The journal of physical chemistry. B

Journal of chemical information and modeling

Journal of the American Chemical Society

This page only lists publications with an associated author ORCID identifier.

Publications

Bella L Grigorenko, Igor V Polyakov, Alexander V Nemukhin
Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. Molecules (Basel, Switzerland) 28 (2) (2023)
Bella Grigorenko, Tatiana Domratcheva, Alexander V Nemukhin
QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules (Basel, Switzerland) 28 (5) (2023)
Bella L Grigorenko, Igor V Polyakov, Alexander V Nemukhin
Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. Molecules (Basel, Switzerland) 28 (2) (2023)
Bella L Grigorenko, Igor V Polyakov, Alexander V Nemukhin
Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. Molecules (Basel, Switzerland) 28 (2) (2023)
Bella Grigorenko, Tatiana Domratcheva, Alexander V Nemukhin
QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules (Basel, Switzerland) 28 (5) (2023)
Bella L Grigorenko, Igor V Polyakov, Maria G Khrenova, Goran Giudetti, Shirin Faraji, Anna I Krylov, 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 (2023)
Bella Grigorenko, Tatiana Domratcheva, Alexander V Nemukhin
QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules (Basel, Switzerland) 28 (5) (2023)
Bella L Grigorenko, Maria G Khrenova, D Dafydd Jones, Alexander V Nemukhin
Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins. Organic & biomolecular chemistry (2023)
Bella L Grigorenko, Igor V Polyakov, Alexander V Nemukhin
Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. Molecules (Basel, Switzerland) 28 (2) (2023)
Goran Giudetti, Igor V Polyakov, Bella L Grigorenko, Shirin Faraji, Alexander V Nemukhin, Anna I Krylov
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 18 (8) (2022)
Bella L Grigorenko, Igor V Polyakov, Alexander V Nemukhin
Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4. The Journal of chemical physics 154 (6) (2021)
Maria G Khrenova, Fedor D Mulashkin, Alexander V Nemukhin
Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation. Journal of chemical information and modeling 61 (10) (2021)
Maria G Khrenova, Anna M Kulakova, 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 61 (3) (2021)
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
Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step. Chemical science 12 (22) (2021)
Maria-Andrea Mroginski, Suliman Adam, Gil S Amoyal, Avishai Barnoy, Ana-Nicoleta Bondar, Veniamin A Borin, Jonathan Richard Church, Tatiana Domratcheva, Bernd Ensing, Francesca Fanelli, Nicolas Ferré, Ofer Filiba, Laura Pedraza-González, Ronald González, Cristina E González-Espinoza, Rajiv Kumar Kar, Lukas Kemmler, Seung Soo Kim, Jacob Kongsted, Anna I Krylov, Yigal Lahav, Michalis Lazaratos, Qays NasserEddin, Isabelle Navizet, Alexander V Nemukhin, Massimo Olivucci, Jógvan Magnus Haugaard Olsen, Alberto Pérez de Alba Ortíz, Elisa Pieri, Aditya G Rao, Young Min Rhee, Niccolò Ricardi, Saumik Sen, Ilia A Solov'yov, Luca De Vico, Tomasz Adam Wesołowski, Christian Wiebeler, Xuchun Yang, Igor Schapiro
Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and photobiology 97 (2) (2021)
Alexandra V Krivitskaya, Maria G Khrenova, 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) 26 (20) (2021)
Maria G Khrenova, Egor S Bulavko, Fedor D Mulashkin, Alexander V Nemukhin
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) 26 (13) (2021)
Bella L Grigorenko, Tatiana Domratcheva, Igor V Polyakov, Alexander V Nemukhin
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 12 (34) (2021)
Tirthendu Sen, Yingying Ma, Igor V Polyakov, Bella L Grigorenko, Alexander V Nemukhin, Anna I Krylov
Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang. The journal of physical chemistry. B 125 (3) (2021)
Bella Grigorenko, Igor Polyakov, Alexander V Nemukhin
Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires. The journal of physical chemistry. B 124 (3) (2020)
Igor V Polyakov, Artem E Kniga, Bella L Grigorenko, Alexander V Nemukhin
Structure of the Brain N-Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling. ACS chemical neuroscience 11 (15) (2020)
Maria G Khrenova, Anna M Kulakova, Alexander V Nemukhin
Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds. Organic & biomolecular chemistry 18 (16) (2020)
Maria G Khrenova, Vladimir G Tsirelson, Alexander V Nemukhin
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 22 (34) (2020)
Maria G Khrenova, Fedor D Mulashkin, Egor S Bulavko, Tatiana M Zakharova, 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 60 (12) (2020)
Bella L Grigorenko, Igor V Polyakov, 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 123 (42) (2019)
Alexander V Nemukhin, Bella L Grigorenko, Maria G Khrenova, Anna I Krylov
Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. The journal of physical chemistry. B 123 (29) (2019)
Maria G Khrenova, Alexander V Nemukhin
Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase. The journal of physical chemistry. B 122 (4) (2018)
Ekaterina D Kots, Maria G Khrenova, Alexander V Nemukhin
Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase. Journal of chemical information and modeling 59 (5) (2018)
Yulia I Meteleshko, Alexander V Nemukhin, Maria G Khrenova
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 18 (1) (2018)
Ekaterina D Kots, Sofya V Lushchekina, Sergey D Varfolomeev, Alexander V Nemukhin
Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase. Journal of chemical information and modeling 57 (8) (2017)
Maria G Khrenova, Yulia I Meteleshko, Alexander V Nemukhin
Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers. The journal of physical chemistry. B 121 (43) (2017)
Maria G Khrenova, Ekaterina D Kots, Sergey D Varfolomeev, Sofya V Lushchekina, Alexander V Nemukhin
Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase. The journal of physical chemistry. B 121 (40) (2017)
Bella L Grigorenko, Anna I Krylov, Alexander V Nemukhin
Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein. Journal of the American Chemical Society 139 (30) (2017)
Maria G Khrenova, Igor V Polyakov, Bella L Grigorenko, Anna I Krylov, Alexander V Nemukhin
Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins. The journal of physical chemistry. B 121 (47) (2017)