Последние публикации

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. Molecular modelling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase
    Polyakov I.V., Khrenova M.G.
    Mol. Phys., 2024, e2397077
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Thio ligand binding in dinitrosyl iron-sulfur complexes: Quantitative structure–activity relationships
    Luzhkov V.B., Krapivin V.B., Sanina N.A., Aldoshin S.M.
    Polyhedron, 2024, 257, 117013
  16. 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
  17. 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
  18. 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
    Dobrolyubov E.O., Manuylov V.M., Krasnoshchekov S.V.
    Moscow Univ. Chem. Bull., 2024, 79(4), 246-256
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Complete genome sequence of new Microbacterium sp. strain ET2, isolated from roots of leafless orchid
    Volynchikova E.A., Khrenova M.G., Panova T.V., Rodin V.A., Zvereva M.I., Tsavkelova E.A.
    Microbiol. Resour. Announc., 2024, 13, e00899
  28. 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
    Richter M., Döring K., Blaas D., Riabova O., Khrenova M., Kazakova E., Egorova A., Makarov V., Schmidtke M.
    Antiv. Res., 2024, 222, 105810
  29. 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
  30. 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
  31. 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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