- Domain mobility in the ORF2p complex revealed by molecular dynamics simulations and big data analysis
Kulakova A.M., Khrenova M.G., Zvereva M.I., Polyakov I.V.
Int. J. Mol. Sci., 2025, 26(1), 73 - The role of conformation states in the heterogeneity of fluorescence decay times in FAD in water-alcohol mixturesConformational dynamics of the enzyme-substrate complex of protein kinase A with pseudosubstrate SP20 and adenosine triphosphate
Volkov D.A., Gorbunova I.A., Yashkov D.V., Sasin M.E., Khrenova M.G., Vasyutinskii O.S.
J. Photochem. Photobiol. A, 2025, 461, 116155
- Conformational dynamics of the enzyme-substrate complex of protein kinase A with pseudosubstrate SP20 and adenosine triphosphate
Mulashkina T.I., Leonova M.S., Khrenova M.G.
Biomeditsinskaya Khimiya, 2024, 70(6), 421-427 - Systematic ab initio calculation of spectroscopic constants for A-reduced rotational effective Hamiltonians of asymmetric top molecules using normal ordering of cylindrical angular momentum operators
Krasnoshchekov S.V., Efremov I.M., Polyakov I.V., Millionshchikov D.V.
J. Chem. Phys., 2024, 161, 234105 - Novel Selectable Marker Sesquiterpenoid Antibiotic Pentalenolactone
Nikandrova A.A., Petriakova A.D., Izzi A.R., Petrosyan G.A., Tashlitsky V.N., Alferova V.A., Panova T.V., Khrenova M.G., Biryukov M.V., Zakalyukina Yu.V., Zvereva M.I., Lukianov D.A., Sergiev P.V.
Int. J. Mol. Sci., 2024, 25(24), 13328 - Biocatalysis: modern problems and applications
Varfolomeev S.D., Švedas V.K., Efremenko E.N., Egorov A.M., Khrenova M.G., Tishkov V.I., Atroshenko D.L., Pometun A.A., Savin S.S., Ugarova N.N., Lomakina G.Yu., Gachok I.V., Lyagin I.V., Muronetz V.I., Sinitsyn A.P., 5, Sinitsyna O.A., Rojhkova A.M., Makhaeva G.F., Bachurin S.O., Lavrik O.I., Zharkov D.O., Yudkina A.V., Panasenko O.M., Baykov A.A., Masson P., Pashirova T.N., Shaihutdinova Z.M., Popova E.V., Tikhomirova V.E., Kost O.A., Kudryashova E.V., Dobryakova N.V., Klyachko N.L., Veselov M.M., Lopukhov A.V., Le-Deygen I.M., Usvaliev A.D., Chudosai I.V., Eremeev N.L., Zvereva M.I., Rubtsova M.Yu, Ulyashova M.M., Presnova G.V., Sigolaeva L.V., Pergushov D.V., Kurochkin I.N., Evtushenko E.G., Boginskaya I.A., Zvyagina Yu Yu, Slipchenko E.A., Kryukova O.V., Sedova M.V., Ryzhikov I.A., Shumyantseva V.V., Koroleva P.I., Bulko T.V., Agafonova L.E., Masamrekh R.A., Filippova T.A., Kuzikov A.V., Savitsky A.P., Shleeva M.O., Solovyev I.D., Marynich N.K.
Russ. Chem. Rev., 2024, 93(12), RCR5144 - Towards accurate machine learning predictions of properties of the P–O bond cleaving in ATP upon enzymatic hydrolysis
Polyakov I.V., Miroshnichenko K.D., Mulashkina T.I., Khrenova M.G.
Mend. Comm., 2024, 34(6), 776-779 - Towards machine learning prediction of the fluorescent protein absorption spectra
Stepanyuk R.A., Polyakov I.V., Kulakova A.M., Marchenko E.I., Khrenova M.G.
Mend. Comm., 2024, 34(6), 788-791 - Determination of the Dipole Moment Variation Upon Excitation in the Chromophore of Green Fluorescent Protein From Molecular Dynamic Trajectories with QM/MM Potentials Using Machine Learning Methods
Zakharova T.M., Kulakova A.M., Krinitsky M.A., Varentsov M.I., Khrenova M.G.
Russ. J. Phys. Chem. A, 2024, 98(11), 2602-2607 - Indole-core inhibitors of influenza a neuraminidase: iterative medicinal chemistry and molecular modeling
Tsedilin A., Schmidtke M., Monakhova N., Leneva I., Falynskova I., Khrenova M., Lane T.R., Ekins S., Makarov V.
Eur. J. Med. Chem., 2024, 277, 119768 - Dynamic features of virus protein 1 and substitutions in the 3-phenyl ring determine the potency and broad-spectrum activity of capsid-binding pyrazolo[3,4-d]pyrimidines against rhinoviruses
Richter M., Khrenova M., Kazakova E., Riabova O., Egorova A., Makarov V., Schmidtke M.
Antiv. Res., 2024, 231, 105993 - Molecular mechanism of thiocyanate dehydrogenase at atomic resolution
Varfolomeeva L.A., Shipkov N.S., Dergousova N.I., Boyko K.M., Khrenova M.G., Tikhonova T.V., Popov V.O.
Int. J. Biol. Macromol., 2024, 279, 135058 - Tool and Algorithm for the Determination of Aptamers in Nanopore Sequencing Data: AptaLong
Grigoryeva M.A., Khrenova M.G., Subach M.F., Voevodin V.V., Zvereva M.I.
Supercomp. Front. Innov., 2024, 11(3), 93-106 - Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study
Mulashkina T.I., Kulakova A.M., Khrenova M.G.
J. Chem. Inf. Model., 2024, 64(18), 7035-7045 - Manifestation of the normal intensity distribution law (NIDL) in the rovibrational emission spectrum of hydroxyl radical
Medvedev E.S., Ermilov A.Yu., Ushakov V.G.
Mol. Phys., 2024, e2395439 - Molecular modelling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase
Polyakov I.V., Khrenova M.G.
Mol. Phys., 2024, e2397077 - Butyrylcholinesterase with altered catalytic triad, acting as a promising bioscavenger against organophosphorus agents
Blinova A.R., Masson P., Kulakova A.M., Grigorenko B.L.
Mol. Phys., 2024, e2387246 - A computational study of possible mechanisms of singlet oxygen generation in miniSOG photoactive protein
Giudetti G., Blinova A.R., Grigorenko B.L., Krylov A.I.
Mol. Phys., 2024, e2396548 - Molecular Basis of Influence of A501X Mutations in Penicillin-Binding Protein 2 of Neisseria gonorrhoeae Strain 35/02 on Ceftriaxone Resistance
Krivitskaya A.V., Kuryshkina M.S., Eremina M.Y., Smirnov I.V., Khrenova M.G.
Int. J. Mol. Sci., 2024, 25(15), 8260 - Saturation Mutagenesis and Molecular Modeling: The Impact of Methionine 182 Substitutions on the Stability of β-Lactamase TEM-1
Grigorenko V.G., Krivitskaya A.V., Khrenova M.G., Rubtsova M.Y., Presnova G.V., Andreeva I.P., Serova O.V., Egorov A.M.
Int. J. Mol. Sci., 2024, 25(14), 7691 - A highly specific aptamer for SARS-CoV-2 Spike protein from the authentic strain
Khrenova M.G., Nikiforova L., Grabovenko F., Orlova N., Sinegubova M., Kolesov D., Zavyalova E., Subach M.F., Polyakov I.V., Zatzepin T., Zvereva M.I.
Org. Biomol. Chem., 2024, 22, 5936-5947 - Thio ligand binding in dinitrosyl iron-sulfur complexes: Quantitative structure–activity relationships
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Polyhedron, 2024, 257, 117013 - Interaction of Copper Clusters with Dioxidine
Ermilov A.Yu, Soloviev A.V., Morosov Yu N., Shabatina T.I.
Moscow Univ. Chem. Bull., 2024, 79(4), 233-238 - The Structure and Dynamics of the Enzyme–Substrate Complex of N-Acetylaspartylglutamate Synthase According to the Computer Simulation Data
Polyakov I.V., Krivitskaya A.V., Khrenova M.G.
Moscow Univ. Chem. Bull., 2024, 79(4), 239-245 - A Prediction of the Vibration-Rotation Absorption Spectra of the D2O Molecule ν2 Band by Solving the Operator Perturbation Theory Direct Problem and a Refinement of the Effective Rotational Hamiltonians
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Moscow Univ. Chem. Bull., 2024, 79(4), 246-256 - A Comparative Study of the Dynamic Behavior of Bacterial Photoregulated Adenylate Cyclases bPAC and OaPAC
Kuryshkina M.S., Kulakova A.M., Moskovsky A.A., Khrenova M.G.
Moscow Univ. Chem. Bull., 2024, 79(4), 257-261 - The Mechanism of Deprotonation of the Amino Group of Glutamate upon Binding to N-Acetylglutamate Synthase
Blinova A.R., Kulakova A.M., Grigorenko B.L.
Moscow Univ. Chem. Bull., 2024, 79(4), 262-267 - Non-Empirical Calculations of Reduced Quartic, Sextic, and Octic Constants of Effective Vibrational–Rotational Hamiltonians, Based on the Operator Perturbation Theory
Efremov I.M., Millionshchikov D.V., Krasnoshchekov S.V.
Russ. J. Phys. Chem. A, 2024, 98(5), 78-88 - Vibrational resonance phenomena of the OCS isotopologues studied by resummation of high-order Rayleigh–Schrödinger perturbation theory
Dobrolyubov E.O., Polyakov I.V., Millionshchikov D.V., Krasnoshchekov S.V.
J. Quant. Spectrosc. Radiat. Transfer, 2024, 316, 108909 - The role of the correlated motion(s) of the chromophore in photoswitching of green and red forms of the photoconvertible fluorescent protein mSAASoti
Gavshina A.V., Solovyev I.D., Khrenova M.G., Boyko K.M., Varfolomeeva L.A., Minyaev M.E., Popov V.O., Savitsky A.P.
Sci. rep., 2024, 14, 8754 - Comparison of the Mechanisms of Hydrolysis of Organophosphates with Good and Poor Leaving Group by Phosphotriesterase from Pseudomonas diminuta
Mulashkina T.I., Kulakova A.M., Nemukhin A.V., Khrenova M.G.
Russ. J. Phys. Chem. A, 2024, 98(2), 283-289 - Modern Methods of Aptamer Chemical Modification and Principles of Aptamer Library Selection
Subach M.F., Khrenova M.G., Zvereva M.I.
Moscow Univ. Chem. Bull., 2024, 79(2), 79-85 - Computer Modeling of the Mechanisms of Enzymatic Reactions: Lessons from 20 Years of Practice
Khrenova M.G., Mulashkina T.I., Kulakova A.M., Polyakov I.V., Nemukhin A.V.
Moscow Univ. Chem. Bull., 2024, 79(2), 86-92 - Complete genome sequence of new Microbacterium sp. strain ET2, isolated from roots of leafless orchid
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Microbiol. Resour. Announc., 2024, 13, e00899 - Molecular mechanism of rhinovirus escape from the Pyrazolo[3,4-d]pyrimidine capsid-binding inhibitor OBR-5-340 via mutations distant from the binding pocket: Derivatives that brake resistance
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Antiv. Res., 2024, 222, 105810 - Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule
Khrenova M.G., Mulashkina T.I., Stepanyuk R.A., Nemukhin A.V.
Mend. Comm., 2024, 34(1), 1-7 - Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins
Grigorenko B.L., Khrenova M.G., Dafydd J.D., Nemukhin A.V.
Org. Biomol. Chem., 2024, 22, 337-347 - Modelling Silver Cluster Complexes with the Antibacterial Medication Dioxidine
Soloviev A.V., Ermilov A.Yu., Morosov Yu.N., Shabatina T.I.
Moscow Univ. Chem. Bull., 2024, 79(1), 21-26
1. Database of Intermediates of Enzyme-Catalyzed Chemical Reactions ENIAD
Moskovsky A.A., Firsov D.A., Khrenova M.G., Mironov V.A., Mulashkina T.I., Kulakova A.M., Nemukhin A.V.
Russ. J. Phys. Chem. A, 2023, 97, 2001-2005
2. In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity
Shilova S.A., Matyuta I.O., Khrenova M.G., et al.
Biochem. J., 2023, 480(16), 1267-1284
3. Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor
Lešnik S., Bren U., Domratcheva T., Bondar A.-N.
J. Chem. Inf. Model., 2023, 63(15), 4732-4748
4. Pyrrolo[2,3-e]indazole as a novel chemotype for both influenza A virus and pneumococcal neuraminidase inhibitors
Egorova A., Richter M., Khrenova M.G., et al.
RSC advanced, 2023, 13(27), 18253-18261
5. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms
Grigorenko B.L., Polyakov I.V., Khrenova M.G., …, Nemukhin A.V.
J. Am. Chem. Soc., 2023, 145(24), 13204-13214
6. Computational Modeling of the Neurofibromin-Stimulated Guanosine Triphosphate Hydrolysis by the KRas Protein
Polyakov I.V., Nemukhin A.V.
Biophysica, 2023, 3(2), 373-384
7. Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form
Boyko K.M., Khrenova M.G., Nikolaeva A.Y., et al.
Int. J. Mol. Sci., 2023, 24(9), 7906
8. Energy profiles of the catalytic cycle of enzymatic reactions and factors determining enzymatic catalysis efficiency
Varfolomeev S.D., Nemukhin A.V., Khrenova M.G., Grigorenko B.L.
Russ. Chem. Bull., 2023, 72, 617-623
9. Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen
Polyakov I.V., Kulakova A.M., Nemukhin A.V.
Biophysica, 2023, 3(2), 252-262
10. Normal ordering of the angular momentum cylindrical ladder operators and their products with Wigner D1,ε functions
Chang X., Millionshchikov D.V., Efremov I.M., Krasnoshchekov S.V.
J. Chem. Phys., 2023, 158, 104802
11. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase
Grigorenko B.L., Domratcheva T.M., Nemukhin A.V.
Molecules, 2023, 28(5), 2405
12. Vibrational resonance analysis of linear molecules using resummation of divergent Rayleigh–Schrödinger perturbation theory series
Chang X., Dobrolyubov E.O., Krasnoshchekov S.V.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2023, 288, 122071
13. To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense
Shilova S.A., Khrenova M.G., Matyuta I.O., et al.
Molecules, 2023, 28(5), 2109
14. Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates
Tikhonova T.V., …, Khrenova M.G., et al.
Structure, 2023, 31(2), 174-184
15. Quantum-mechanical insights into the anisotropic response of the cryptochrome radical pair to a weak magnetic field
Bezchastnov V., Domratcheva T.
J. Chem. Phys., 2023, 158, 034303
16. Spectroscopic and Computational Observation of Glutamine Tautomerization in the Blue Light Sensing Using Flavin Domain Photoreaction
Hontani Yu., Mehlhorn J., Domratcheva T.M., et al.
J. Am. Chem. Soc., 2023, 145(2), 1040-1052
17. Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang
Grigorenko B.L., Polyakov I.V., Nemukhin A.V.
Molecules, 2023, 28(2), 505
18. Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling
Krivitskaya A.V., Khrenova M.G.
Int. J. Mol. Sci., 2023, 24(1), 176
1. Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations
Weik M., Domratcheva T.
Current Opinion in Structural Biology, 2022, 77, 102496
2. Computational Modeling of the Interaction of Molecular Oxygen with the Flavin-dependent Enzyme RutA
Polyakov I.V., Domratcheva T.M., Kulakova A.M., Nemukhin A.V., Grigorenko B.L.
Supercomputing Frontiers and Innovations, 2022, 9(2), 46-55
3. Computational Characterization of N-acetylaspartylglutamate Synthetase: From the Protein Primary Sequence to Plausible Catalytic Mechanism
Polyakov I.V., Kniga A.E., Nemukhin A.V.
Supercomputing Frontiers and Innovations, 2022, 9(2), 4-13
4. Predicting the Activity of Boronate Inhibitors Against Metallo-β-lactamase Enzymes
Levina E.O., Khrenova M.G., Tsirelson V.G.
Supercomputing Frontiers and Innovations, 2022, 9(2), 14-32
5. Mechanism of chemical reactions in the active site of aspartate N-acetyltransferase NAT8L revealed by molecular modeling
Polyakov I.V., Khrenova M.G., Grigorenko B.L., Nemukhin A.V.
Mend. Comm., 2022, 32(6), 739-741
6. Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen
Polyakov I.V., Nemukhin A.V., Domratcheva T.M., Kulakova A.M., Grigorenko B.L.
Mol. Inf., 2022, 42(2), 2200175
7. Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases
Krivitskaya A.V., Khrenova M.G.
Molecules, 2022, 27(20), 7031
8. Molecular Dynamics of Enzyme-Substrate Complexes in Guanosine Trifosphate-Binding Proteins
Khrenova M.G., Polyakov I.V., Nemukhin A.V.
Russ. J. Phys. Chem. B, 2022, 16, 455-460
9. Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement
Adam V., …, Domratcheva T.M., et al.
Chem. Phys. Chem., 2022, 23(19), e202200192
10. Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism
Khrenova M.G., Panova T.V., Rodin V.A., et al.
Int. J. Mol. Sci., 2022, 23(15), 8569
11. How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur
Giudetti G., Polyakov I.V., Grigorenko B.L., …, Nemukhin A.V., et al.
J. Chem. Theory Comput., 2022, 18(8), 5056-5067
12. Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution
Krivitskaya A.V., Khrenova M.G.
J. Chem. Inf. Model., 2022, 62(24), 6519-6529
13. Influence of the leaving group on the mechanism of hydrolysis of organophosphorus compounds by phosphotriesterase from bacterium Pseudomonas diminuta
Kulakova A.M., Mulashkina T.I., Nemukhin A.V., Khrenova M.G.
Russ. Chem. Bull., 2022, 71, 921-926
14. Molecular modeling of ceftriaxone activation in the active sites of penicillin-binding proteins 2
Krivitskaya A.V., Khrenova M.G.
Russ. Chem. Bull., 2022, 71, 915-920
15. First biphotochromic fluorescent protein moxSAASoti stabilized for oxidizing environment
Marynich N.K., Khrenova M.G., Gavshina A.V., et al.
Sci. Rep., 2022, 12, 7862
16. A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine
Boyko K.M., …, Khrenova M.G. et al
Crystals, 2022, 12(5), 619
17. Spontaneous Reactivation of OPC-Inhibited BChE Mutants: Modeling of Mechanisms
Lushchekina S.V., Nemukhin A.V., Polyakov I.V., …, Grigorenko B.L. et al.
Russ. J. Phys. Chem. B, 2022, 16, 103-108
18. Keto-enol tautomerism from the electron delocalization perspective
Levina E.O., Khrenova M.G., Astakhov A.A., et al.
Int. J. Comp. Chem., 2022, 43(15), 1000-1010
19. Complex of HIV-1 Integrase with Cellular Ku Protein: Interaction Interface and Search for Inhibitors
Ilgova E., Galkin S., Khrenova M.G., et al.
Int. J. Mol. Sci., 2022, 23(6), 2908
20. Non-Equivalence of Monomers in the Dimeric Structure of a Bacterial Photoactivated Adenylyl Cyclase
Kulakova A.M., Khrenova M.G., Nemukhin A.V.
Biophysics, 2022, 67, 895-901
21. Fundamental studies of vibrational resonance phenomena by multivalued resummation of the divergent Rayleigh–Schrödinger perturbation theory series: deciphering polyad structures of three H216O isotopologues
Chang X., Dobrolyubov E.O., Krasnoshchekov S.V.
Phys. Chem. Chem. Phys., 2022, 24, 6655-6675
22. Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections
Grigorenko V.G., Khrenova M.G., Andreeva I.P., et al.
Int. J. Mol. Sci., 2022, 23(3), 1834
23. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers
Mironov V.A., Shchugoreva I.A., …, Moskovsky A.A., et al.
Chemistry — A European Journal, 2022, 28(12), e202104481
24. Non-empirical analysis of isotopic shifts and resonance effects in the infrared high-resolution spectrum of freon-22 (CHF2Cl), enriched with 13C
Krasnoshchekov S.V., Gainullin I.K., Laptev V.B., et al.
Optics and Spectroscopy, 2022, 130(1), 8-18
1. The role of cysteine residues in the allosteric modulation of the chromophore phototransformations of biphotochromic fluorescent protein SAASoti
Gavshina A.V., Marynich N.K., Khrenova M.G., et al.
Sci. Rep., 2021, 11, 24134
2. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift
Subach O.M., Vlaskina A.V., …, Khrenova M.G., et al
Int. J. Mol. Sci., 2021, 22(23), 12887
3. Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2
Nemukhin A.V., Grigorenko B.L., Lushchekina S.V., et al.
Russ. Chem. Bull., 2021, 70, 2084-2089
4. Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase
Krivitskaya A.V., Khrenova M.G., Nemukhin A.V.
Molecules, 2021, 26(20), 6280
5. Infrared vibrational spectra and absolute intensities of fundamental bands of bis(trifluoromethyl)ketene: Ab initio interpretation using the second order operator Van Vleck perturbation theory
Krasnoshchekov S.V., Laptev V.B., Gainullin I.K.
Journal of Quantitative Spectroscopy and Radative Transfer, 2021, 276, 107952
6. Computer Modeling of Structures of Reversibly Switchable Fluorescent Proteins with LOV Domains
Meteleshko Yu.I., Khrenova M.G., Nemukhin A.V.
Crystallography Reports, 2021, 66, 815-818
7. Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation
Khrenova M.G., Mulashkin F.D., Nemukhin A.V.
J. Chem. Inf. Model., 2021, 61(10), 5125-5132
8. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Morozov D.I., Mironov V.A., Moryachkov R.V., et al.
Molecular therapy. Nucleic acids, 2021, 25, 316-327
9. Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2
Grigorenko B.L., Domratcheva T.M., Polyakov I.V., Nemukhin A.V.
J. Phys. Chem. Lett., 2021, 12(34), 8263-8271
10. The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme
Bakunova A.K., Nikolaeva A.Yu., …, Khrenova M.G., et al.
Molecules, 2021, 26(16), 5053
11. Relationship Between Matrix Metalloproteinase-2 Inhibition Constants With APP-IP Oligopeptide and Its Mutant Forms and Electronic Binding Descriptors
Kulakova A.M., Khrenova M.G.
Russ. J. Phys. Chem. B, 2021, 15, 394-398
12. CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs
Giannos T., Lešnik S., …, Domratcheva T.M., et al.
J. Chem. Inf. Model., 2021, 61(8), 3964-3977
13. Molecular Modeling Reveals the Mechanism of Ran-RanGAP-Catalyzed Guanosine Triphosphate Hydrolysis without an Arginine Finger
Khrenova M.G., Grigorenko B.L., Nemukhin A.V.
ACS Catal., 2021, 11(15), 8985-8998
14. Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials
Khrenova M.G., Bulavko E.S., Mulashkin F.D., Nemukhin A.V.
Molecules, 2021, 26(13), 3998
15. Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices
Xu X., …, Grigorenko B.L., Nemukhin A.V., et al.
Angewandte Chemie, 2021, 60(37), 20184-20189
16. Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1
Kulakova A.M., Khrenova M.G., Nemukhin A.V.
Biomeditsinskaya Khimiya, 2021, 67(3), 300-305
17. In silico specificity determination of neoantigen-reactive T-lymphocytes
Kniga A.E., Polyakov I.V., Nemukhin A.V.
Biomeditsinskaya Khimiya, 2021, 67(3), 251-258
18. Applying joint theoretical experimental research to aptamer modeling
Shchugoreva I. A., Artyushenko P. V., …, Mironov V.A., et al.
Siberian Medical Review., 2021, 2, 105-106
19. The O to S substitution in urea brings inhibition activity against thiocyanate dehydrogenase
Khrenova M.G., Soloveva A.Yu., Varfolomeeva L.A., et al.
Mend. Comm., 2021, 31(3), 373-375
20. Model of the RNA Polymerase Complex of the SARS-CoV-2 Virus with Favipiravir
Polyakov I.V., Grigorenko B.L., Nemukhin A.V.
Russ. J. Phys. Chem. B, 2021, 15, 103-107
21. Keto-enol tautomerism of the 4,5-dimethyl-2-(2′-hydroxyphenyl)imidazole in water solution: Modeling equilibrium between neutral forms and accurate assignment of the absorption bands
Kapusta D.P., Mulashkin F.D., Khrenova M.G.
International Journal of Quantum Chemistry, 2021, 121(8), e26577
22. Mechanism and dynamics of fatty acid photodecarboxylase
Sorigué D., Hadjidemetriou K., …, Domratcheva T.M., et al.
Science, 2021, 372(6538), eabd5687
23. Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling
Krivitskaya A.V., Khrenova M.G.
Molecules, 2021, 26(7), 2026
24. Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2
Artyushenko P.V., Mironov V.A., Morozov D.I., et al.
Siberian Medical Review., 2021, 2, 66-67
25. Molecular mechanism of the cesium and rubidium selective binding to the calix[4]arene revealed by Born–Oppenheimer molecular dynamics simulation and electron density analysis
Kulakova A.M., Khrenova M.G.
Mend. Comm., 2021, 31(2), 185-187
26. Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step
Auhim H.S., Grigorenko B.L., …, Polyakov I.V., …, Nemukhin A.V., et al.
Chem. Sci., 2021, 12, 7735-7745
27. Hypofluorous acid (HOF): A molecule with a rare (1,-2,-1) vibrational resonance and (8,3,2) polyad structure revealed by Padé-Hermite resummation of divergent Rayleigh-Schrödinger perturbation theory series
Krasnoshchekov S.V., Dobrolyubov E.O., Chang X.
Journal of Quantitative Spectroscopy and Radative Transfer, 2021, 268, 107620
28. Luminescent Zero-Dimensional Hybrid Lead Thiohalide Nanostructures for High Quantum Yield and Broadband Excitation
Golovnev N.N., Aleksandrovsky A.S., …, Mironov V.A., et al.
ACS Appl. Nano Mater., 2021, 4(4), 3654-3663
29. 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
Khrenova M.G., Kulakova A.M., Nemukhin A.V.
J. Chem. Inf. Model., 2021, 61(3), 1215-1225
30. The explicit role of electron exchange in the hydrogen bonded molecular complexes
Levina E.O., Khrenova M.G., Tsirelson V.G.
J. Comp. Chem., 2021, 42(12), 870-882
31. Frontiers in Multiscale Modeling of Photoreceptor Proteins
Mroginski M.-A., Adam S., …, Domratcheva T.M., …, Nemukhin A.V., et al.
Photochem. Photobio., 2021, 97(2), 243-269
32. Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4
Grigorenko B.L., Polyakov I.V., Nemukhin A.V.
J. Chem. Phys., 2021, 154, 65101
33. Metallo-β-Lactamases: Influence of the Active Site Structure on the Mechanisms of Antibiotic Resistance and Inhibition
Levina E.O., Khrenova M.G.
Biochemistry(Moscow), 2021, 86, S24-S37
34. Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang
Sen T., Ma Y., Polyakov I.V., Grigorenko B.L., Nemukhin A.V., et al.
J. Phys. Chem. B, 2021, 125(3), 757-770
1. Structural and Transport Features of sp-Carbon Films Synthesized by Pulsed Plasma Deposition on Various Metal Substrates
Ivanenko I.P., Krasnoshekov S.V., Pavlikov A.V., et al.
J. Surf. Inv., 2020, 14, 1240-1247
2. Computer Modeling of N-Acetylglutamate Synthase: From Primary Structure to Elemental Stages of Catalysis
Polyakov I.V., Kniga A.E., Grigorenko B.L., Nemukhin A.V., et al.
Doklady Biochem. Boiphys., 2020, 495, 334-337
3. Fundamental Analysis of Singular and Resonance Phenomena in Vibrational Polyads of the Difluorosilylene Molecule
Krasnoshchekov S.V., Dobrolyubov E.O., Chang X.
Optics and Spectroscopy, 2020, 128, 1927-1938
4. Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores
Khrenova M.G., Mulashkin F.D., Bulavko E.S., Zakharova T.M., Nemukhin A.V.
J. Chem. Inf. Model., 2020, 60(12), 6288-6297
5. Computational Modeling of the SARS-CoV-2 Main Protease Inhibition by the Covalent Binding of Prospective Drug Molecules
Nemukhin A.V., Grigorenko B.L., Polyakov I.V., Lushchekina S.V.
Supercomputing Frontiers and Innovations, 2020, 7(3), 25-32
6. Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease
Khrenova M.G., Tsirelson V.G., Nemukhin A.V.
Supercomputing Frontiers and Innovations, 2020, 7(3), 33-40
7. Overtone spectroscopy of v(C=O) stretching vibration of hexafluoroacetone: Experimental and ab initio determination of peak positions, absolute intensities, and band shapes
Krasnoshchekov S.V., Laptev V.B., Klimin S.A., et al.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2020, 238, 118396
8. Benchmark studies of hydrogen bond governing reactivity of cephalosporins in L1 metallo-β-lactamase: Efficient and reliable QSPR equations
Khrenova M.G., Levina E.O., Tsirelson V.G.
Int. J. Quant. Chem., 2020, 121(4), e265451
9. Discrimination of enzyme–substrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2
Khrenova M.G., Nemukhin A.V., Tsirelson V.G.
Mend. Comm., 2020, 30(5), 583-585
10. Dynamical properties of enzyme–substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors
Khrenova M.G., Tsirelson V.G., Nemukhin A.V.
Phys. Chem. Chem. Phys., 2020, 22, 19069-19079
11. Structure of the Brain N-Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling
Polyakov I.V., Kniga A.E., Grigorenko B.L., Nemukhin A.V.
ACS Chem. Neurosci., 2020, 11(15), 2296-2302
12. Normal ordering of the su(1, 1) ladder operators for the quasi-number states of the Morse oscillator
Chang X., Krasnoshchekov S.V., Pupyshev V.I., et al.
Phys. Lett. A, 2020, 384(19), 126493
13. Intermediates of the Autocatalytic Reaction of the Formation of a Chromophore in a Green Fluorescent Protein
Grigorenko B.L., Khrenova M.G., Kulakova A.M., Nemukhin A.V.
Russ. J. Phys. Chem. B, 2020, 14, 457-461
14. Estimation of Dissociation Constant of ARS-1620 Complex with KRASG12C Protein by Molecular Modeling
Kulakova A.M., Zakharova T.M., Mulashkin F.D., Terekhova E.O., Khrenova M.G.
Moscow University Chemistry Bulletin, 2020, 75, 72-76
15. Modeling the Tautomeric Equilibrium and Absorption Spectrum of 4,5-Dimethyl-2-(2′-hydroxyphenyl)imidazole
Kapusta D.P., Kulakova A.M., Khrenova M.G.
Russ. J. Phys. Chem. A, 2020, 94, 945-950
16. Theoretical Vibrational Spectra of Reaction Intermediates in the Active Site of Guanosine Triphosphate Binding Proteins
Grigorenko B.L., Nemukhin A.V.
Russ. J. Phys. Chem. A, 2020, 94, 914-918
17. Theoretical characterization of the photochemical reaction CO2 + O(3P) → CO + O2 related to experiments in solid krypton
Grigorenko B.L., Duarte L., Polyakov I.V., Nemukhin A.V.
Chem. Phys. Lett., 2020, 746, 137303
18. Recent developments in the general atomic and molecular electronic structure system
Barca G.M.J., Bertoni C., …, Mironov V.A., et al.
J. Chem. Phys., 2020, 152(15), 154102
19. Rigorous vibrational Fermi resonance criterion revealed: two different approaches yield the same result
Krasnoshchekov S.V., Dobrolyubov E.O., Syzgantseva M.A., et al.
Molecular Physics, 2020, 118(11), 1-7
20. Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds
Khrenova M.G., Kulakova A.M., Nemukhin A.V.
Org. Biomol. Chem., 2020, 18, 3069-3081
21. Large-Scale Prediction of the ARS Family Inhibitors of the Oncogenic KRASG12C Mutant
Kulakova A.M., Popinako A.V., Khrenova M.G.
Lecture Notes in Computer Science, 2020, 11958, 348-355
22. Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires
Grigorenko B.L., Polyakov I.V., Nemukhin A.V.
J. Phys. Chem. B, 2020, 124(3), 451-460
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