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Последние публикации

  1. High-resolution ro-vibrational analysis of HCFC-22: Deciphering 𝜈4 and 2𝜈6 bands of 12CH35ClF2 and 𝜈4 band of 13CH35ClF2 species
    Dobrolyubov E.O., Efremov I.M., Krasnoshchekov S.V., Polyakov I.V., Laptev V.B., Klimin S.A., Millionshchikov D.V., Naumenko O.V.
    J. Quant. Spectrosc. Radiat. Transfer, 2026, 348, 109721
  2. Nanopore Sequencing Reveals Microbial Community Compositions on Microplastic in the Setun River of the Moscow Region
    Eremin A., Trefilov V., Sergeev A., Lisina A., Panova T., Berkovich A., Khrenova M.G., Sazonov A., Efimova A., Zvereva M. 
     Environments, 2026, 13(1), 26
  3. Effect of the avoided crossing on the rovibrational energy levels, resonances, and predissociation lifetimes within the ground and first excited electronic states of lithium fluoride
    Ushakov V.G., Ermilov A.Yu., Medvedev E.S.
    J. Quant. Spectrosc. Radiat. Transfer, 2026, 352, 109811
  4. The HITRAN2024 molecular spectroscopic database
    Gordon I.E., Rothman L.S., Hargreaves R.J., Gomez F.M., Bertin T., Hill C., Kochanov R.V., Tan Y., Wcisło P., Makhnev V.Yu, Bernath P.F., Birk M., Boudon V., Campargue A., Coustenis A., Drouin B.J., Gamache R.R., Hodges J.T., Jacquemart D., Mlawer E.J., Nikitin A.V., Perevalov V.I., Rotger M., Robert S., Tennyson J., Toon G.C., Tran H., Tyuterev V.G., Adkins E.M., Barbe A., Bailey D.M., Bielska K., Bizzocchi L., Blake T.A., Bowesman C.A., Cacciani P., Čermák P., Császár A.G., Denis L., Egbert S.C., Egorov O., Ermilov A.Yu., Fleisher A.J., Fleurbaey H., Foltynowicz A., Furtenbacher T., Germann M., Guest E.R., Harrison J.J., Hartmann J.M., Hjältén A., Hu S.M., Huang X., Johnson T.J., Jóźwiak H., Kassi S., Khan M.V., Kwabia-Tchana F., Lee T.J., Lisak D., Liu A.W., Lyulin O.M., Malarich N.A., Manceron L., Marinina A.A., Massie S.T., Mascio J., Medvedev E.S., Meshkov V.V., Mellau G.Ch, Melosso M., Mikhailenko S.N., Mondelain D., Muller H.S.P., O’Donnell M., Owens A., Perrin A., Polyansky O.L., Raston P.L., Reed Z.D., Rey M., Richard C., Reiker G.B., Röske C., Sharpe S.W., Starikova E., Stolarczyk N., Stolyarov A.V., Sung K., Tamassia F., Terragni J., Ushakov V.G., Vasilchenko S., Vispoel B., Vodopyanov K.L., Wagner G., Wójtewicz S., Yurchenko S.N., Zobov N.F.
    J. Quant. Spectrosc. Radiat. Transfer, 2026, 352, 109807
  1. Tools and Algorithms for Nanopore Sequencing Data Analysis in Genomics, Metagenomics, and Epigenomics
    Eremin A.A., Sergeev A.V., Zvereva M.E., Khrenova M.G.
    Math. Biol. Bioinf., 2025, 20(2), 588-624
  2. Dynamic Features Control the Stabilization of the Green and Red Forms of the Chromophore in AzamiGreen Fluorescent Protein Variants
    Krapivin V.B., Stepanyuk R.A., Khrenova M.G.
    Biophysica, 2025, 5(4), 53
  3. Characterization of Bacillus velezensis EV17 and K-3618 and Their Polyketide Antibiotic Oxydifficidin, an Inhibitor of Prokaryotic Translation with Low Cytotoxicity
    Chernyshova A.P., Marina V.I., Tereshchenkov A.G., Sagitova V.E., Kryakvin M.A., Dagaev N.D., Yurchenko E.G., Arzamazova K.A., Guglya E.B., Belozerova O.A., Kovalchuk S.I., Baranova M.N., Kudzhaev A.M., Shikov A.E., Romanenko M.N., Rudenko A.Yu., Chebotar V.K., Gancheva M.S., Baganova M.E., Biryukov M.V., Panova T.V., Khrenova M.G., Tashlitsky V.N., Sumbatyan N.V., Zakalyukina Yu.V., Antonets K.S., Nizhnikov A.A., Polshakov V.I., Terekhov S.S., Zvereva M.I., Dontsova O.A., Sergiev P.V., Alferova V.A., Lukianov D.A.
    Int. J. Mol. Sci., 2025, 26(24), 11777
  4. Dynamic protonation states and vacancy migration modulate glutaminase C catalysis: essential role of Lys481 and Tyr466
    Polyakov I.V., Khrenova M.G.
    Russ. Chem. Bull., 2025, 74, 2367-2376
  5. Boronic acids: broad specificity of inhibition of penicillin-binding proteins and β-lactamases conferring bacterial antibiotic resistance
    Egorov A.M., Ulyashova M.M., Khrenova M.G., Kholmanskikh D.D., Rubtsova M.Yu.      
    Russ. Chem. Bull., 2025, 74, 2332-2359
  6. Mechanism for Nucleotidyl Transfer in LINE-1 ORF2p Revealed by QM/MM Simulations
    Polyakov I.V., Miroshnichenko K.D., Mulashkina T.I., Kulakova A.M., Khrenova M.G.
    Int. J. Mol. Sci., 2025, 26(17), 8661
  7. Enabling Fluorescence Lifetime Imaging Multiplexing Using UnaG through Its Modification with Canonical and Noncanonical Amino Acids
    Terekhova V.V., Bodunova D.V., Gorokhov E.S., Tsoraev G.V., Sidorenko S.V., Vasilev R.A., Levitskii S.A., Kamenski P.A., Loktyushkin A.V., Kovalchuk S.I., Lukashev E.P., Bogdanova Yu.A., Bogdanov A.M., Mulashkina T.I., Khrenova M.G., Gvozdev D.A., Yakimov B.P., Shirshin E.A., Friedrich T., Budisa N., Stepanov A.V., Sluchanko N.N., Baranov M.S., Maksimov E.G., Kirpichnikov M.P.
    ACS Sensors, 2025
  8. CopC as a potential metallochaperone delivering copper ions to the active site of a thiocyanate dehydrogenase
    Solovieva A.Y., Kulikova O.G., Varfolomeeva L.A., Dergousova N.I., Boyko K.M., Khrenova M.G., Tikhonova T.V., Popov V.O.
    Int. J. Biol. Macromol., 2025, 322, 146801
  9. Juxtaposing the fourth order vibrational operator perturbation theory CVPT(4) and the adaptive VCI (A-VCI): Accuracy, vibrational resonances and polyads of C2H4 and C2D4
    Le Bris V., Krasnoshchekov S.V., Dobrolyubov E.O., Efremov I.M., Polyakov I.V., Coulaud O., Beque D.
    J. Quant. Spectrosc. Radiat. Transfer, 2025, 346, 1-24
  10. Special Issue: “Advanced Research on Molecular Modeling of Protein Structure and Functions”
    Khrenova M.G.
    Int. J. Mol. Sci., 2025, 26(16), 7916
  11. NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency
    Grigoryeva M.A., Khrenova M.G., Zvereva M.I.
    J. Bioinf. Comput. Biol., 2025, 23(4), 2550011
  12. Enzymatic P-O bond cleavage: criteria of dissociative and associative mechanisms
    Mulashkina T.I., Kulakova A.M., Khrenova A.M.
    J. Chem. Inf. Model., 2025, 65(15), 8181-8193
  13. QM/MM insights into catalytic activation of firefly luciferin by MgATP
    Blinova A.R., Domratcheva T.M., Grigorenko B.L.
    Mol. Catal., 2025, 115316
  14. Microscopic Mechanism of the Denaturation of Proteins and Nucleic Acids of Pseudomonas Aeruginosa Resonantly Absorbing 6-µm Femtosecond Laser Pulse
    Kudryashov S.I., Shelygina S.N., Kompanets V.O., Chekalin S.V., Efremov I.M., Stolyarov A.V., Tolordava E.R.
    JETP Letters, 2025, 122(3), 197-202
  15. Substrate Activation Efficiency in Active Sites of Hydrolases Determined by QM/MM Molecular Dynamics and Neural Networks
    Polyakov I.V., Meteleshko Yu.I., Mulashkina T.I., Varentsov M.I., Krinitskiy M.A., Khrenova M.G.
    Int. J. Mol. Sci., 2025, 26(11), 5097
  16. Formation of a triple complex of viral capsid protein 1 and two capsid-binding inhibitors explains synergistic interactions observed in combination studies with rhinoviruses
    Richter M., Khrenova M.G., Riabova O.S., Makarov V., Schmidtke M.
    Biomed. Pharm., 2025, 188, 118193
  17. Recent Technology Trends in High-Performance Computing: Quantifying the Divergence of Top and the Rest
    Konyukhov S.S., Moskovsky A.A.
    Supercomp. Front. Innov., 2025, 12 (1), 5-18
  18. Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly
    Eremin A., Sergeev A., Kopylov A., Rodin V., Malyshev D., Panova T., Polyakov I., Zvereva M.
    Frontiers in genetics, 2025, 16, 1574332
  19. 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

  20. Interaction of Silver Clusters with 7-Aminocholesterol: Non-Empirical Study
    Gromova Ya.A., Solovyev A.V., Ermilov A.Yu., Shabatina T.I.
    Moscow Univ. Chem. Bull., 2025, 80(2), 70-75 

  21. DFT Study of Dioxidine Oligomer Formation in the Gas Phase and CO2 Environment
    Soloviev A.V., Ermilov A.Yu., Morozov Yu.N., Astashova I.V.,  Filinovskiy A.V., Shabatina T.I.
    Moscow Univ. Chem. Bull., 2025, 80(2), 76-82

  22. Topological representation of layered hybrid lead halides for machine learning using universal clusters
    Marchenko E.I., Khrenova M.G., Korolev V.V., Goodilin E.A., Tarasov A.B.
    Mend. Comm., 2025, 35(4), 383-385

  23. Molecular mechanism of nitrocefin hydrolysis by the L1 metallo-β-lactamase: a benchmark study
    Krivitskaya A.V., Polyakov I.V., Khrenova M.G.
    Mol. Phys., 2025, e2456688

  24. Three-states model for calculating the X-X rovibrational transition intensities in hydroxyl radical
    Ushakov V.G., Ermilov A.Yu., Medvedev E.S.
    J. Mol. Spectrosc., 2025, 407, 111977

  25. Three-states model for calculating the X-X rovibrational transition intensities in hydroxyl radical (Erratum)
    Ushakov V.G., Ermilov A.Yu., Medvedev E.S.
    J. Mol. Spectrosc., 2025, 408, 111996

  26. Engineering hydrogen bonding at tyrosine-201 in the orange carotenoid protein using halogenated analogues
    Tsoraev G.V., Bukhanko A.Y., Mamchur A.A., Surkov M.M., Sidorenko S.V., Moldenhauer M., Tseng H.-W., Petrovskaya L.E., Cherepanov D.A., Shelaev I.V., Gostev F.E., Blinova A.R., Grigorenko B.L., Yaroshevich I.A., Nadtochenko V.A., Budisa N., Kamenski P., Friedrich Th., Maksimov E.G.
    Photosynth. Res., 2025, 163(1), 10

  27. 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
  1. 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
  2. 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
  3. 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
  4. 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., 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. Molecular modelling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase
    Polyakov I.V., Khrenova M.G.
    Mol. Phys., 2024, e2397077
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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., Nikolaeva A.Y., Klyachko N.L., Minyaev M.E., Khomutov A.R., Boyko K.M., Popov V.O., Bezsudnova E.Yu.
    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., Dietrich E., Tsedilin A., Kazakova E., Lepioshkin A., Jahn B., Chernyshev V., Schmidtke M., Makarov V.
    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., Giudetti G., Faraji Sh., Krylov A., 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., Dorovatovskii P.V., Vlaskina A.V., Subach O.M., Popov V.O., Subach F.V.
    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., Nikolaeva A.Y., Rakitina T.V., Klyachko N.L., Minyaev M.E., Boyko K.M., Popov V.O., Bezsudnova E.Yu.
    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., Osipov E.M., Dergousova N.I., Boyko K.M., Elizarov I.M., Gavrilov S.N., Khrenova M.G., Robb F.T., Solovieva A.Y., Bonch-Osmolovskaya E.A., Popov V.O.
    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., Beck S., Kloz M., Hegemann P., Mathes T., Kennis J.T.M.
    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. 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
  2. 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
  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., Hadjidemetriou K., Jensen N., Shoeman R. L., Woodhouse J., Aquila A., Banneville A.-S., Barends T. R. M., Bezchastnov V., Boutet S., Byrdin M., Cammarata M., Carbajo S., Christou N. E., Coquelle N., De la Mora E., El Khatib M., Moreno Chicano T., Doak R. B., Fieschi F., Foucar L., Glushonkov O., Gorel A., Grünbein M. L., Hilpert M., Hunter M., Kloos M., Koglin J. E., Lane T. J., Liang M., Mantovanelli A., Nass K., Nass Kovacs G., Owada S., Roome C. M., Schirò G., Seaberg M., Stricker M., Thépaut M., Tono K., Ueda K., Uriarte L. M., You D., Zala N., Domratcheva T., Jakobs S., Sliwa M., Schlichting I., Colletier J.-P., Bourgeois D., Weik M.
    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., Kryakvin M.A., Lukyanov D.A., Osterman I.A., Zvereva M.I.
    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., Faraji Sh., Nemukhin A.V., Krylov A.I.
    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., Solovyev I.D., Savitsky A.P.
    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., Matyuta I.O., Nikolaeva A.Y., Rakitina T.V., Popov V.O., Bezsudnova E.Yu., Khrenova M.G.
    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., Masson P., Varfolomeev S.D., Grigorenko B.L.
    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., Tsirelson V.G.
    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., Serebryakova M., Gottikh M., Anisenko A.
    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., Rubtsova M.Yu., Lev A.I., Novikova T.S., Detusheva E.V., Fursova N.K., Dyatlov I.A., Egorov A.M.
    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., Artyushenko P.V., Morozov D., Borbone N., Oliviero G., Zamay T.N., Moryachkov R.V., Kolovskaya O.S., Lukyanenko K.A., Song Y., Merkuleva I.A., Zabluda V.N., Peters G., Koroleva L.S., Veprintsev D.V., Glazyrin Y.E., Volosnikova E.A., Belenkaya S.V., Esina T.I., Isaeva A.A., Nesmeyanova V.S., Shanshin D.V., Berlina A.N., Komova N.S., Svetlichnyi V.A., Silnikov V.N., Shcherbakov D.N., Zamay G.S., Zamay S.S., Smolyarova T., Tikhonova E.P., Chen K.H.-C., Jeng U.-S., Condorelli G., de Franciscis V., Groenhof G., Yang C., Moskovsky A.A., Fedorov D.G., Tomilin F.N., Tan W., Alexeev Y., Berezovski M.V., Kichkailo A.S.
    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., Klimin S.A.
    Optics and Spectroscopy, 2022, 130(1), 8-18
  1. Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2
    Nemukhin A.V., Grigorenko B.L., Lushchekina S.V., Varfolomeev S.D.
    Russ. Chem. Bull., 2021, 70, 2084-2089
  2. 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., Solovyev I.D., Savitsky A.P. 
    Sci. Rep., 2021, 11, 24134
  3. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift
    Subach O.M., Vlaskina A.V., Agapova Yu.K., Dorovatovskii P.V., Nikolaeva A.Y., Ivashkona O.I., Popov V.O., Piatkevich K.D., Khrenova M.G., Smirnova T.A., Boyko K.M., Subach F.V.
    Int. J. Mol. Sci., 2021, 22(23), 12887
  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., Shchugoreva I.A., Artyushenko P.V., Zamay G.S., Kolovskaya O.S., Zamay T.N., Krat A.V., Molodenskiy D.S., Zabluda V.N., Veprintsev D.V., Sokolov A.E., Zukov R.A., Berezovski M.V., Tomilin F.N., Fedorov D.G., Alexeev Y., Kichkailo A.S.
    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., Rakitina T.V., Isaikina T.Y., Khrenova M.G., Boyko K.M., Popov V.O., Bezsudnova E.Yu.
    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., Bren U., Hodošček M., Domratcheva T.M., Bondar A.-N.
    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., Bowen B. J., Gwyther R. E. A., Freeley M., Grigorenko B.L., Nemukhin A. V., Eklöf-Österberg J., Moth-Poulsen K., Jones D. D., Palma M.
    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., Tomilin E.N., Morozov D., Mironov V.A., Moryachkov R.V., Kichkailo A.S.
    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., Tikhonova T.V., Popov V.O.
    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., Blangy S., Gotthard G., Bonvalet A., Coquelle N., Samire P., Aleksandrov A., Antonucci L., Benachir A., Boutet S., Byrdin M., Cammarata M., Carbajo S., Cuiné S., Doak R. B., Foucar L., Gorel A., Grünbein M., Hartmann E., Hienerwadel R., Hilpert M., Kloos M., Lane T. J., Légeret B., Legrand P., Li-Beisson Y., Moulin S. L. Y., Nurizzo D., Peltier G., Schirò G., Shoeman R. L., Sliwa M., Solinas X., Zhuang B., Barends T. R. M., Colletier J.-P., Joffre M., Royant A., Berthomieu C., Weik M., Domratcheva T.M., Brettel K., Vos M. H., Schlichting I., Arnoux P., Müller P., Beisson F.
    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., Shchugoreva I.A., Borbone N., Tomilin F.N., Kichkailo A.S.
    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., Harris T.K., Aksakal O.E., Polyakov I.V., Berry C., dos Passos Gomes G., Alabugin I.V., Rizkallah P.J., Nemukhin A.V., Jones D.D.
    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.
    J. Quant. Spectrosc. Radiat. 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., Gerasimona M.A., Tomilin F.N., Mironov V.A., Demina A.V., Zia Zh., Molokeev M.S.
    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., Amoyal G. S., Barnoy A., Bondar A.-N., Borin V. A., Church J. R., Domratcheva T.M., Ensing B., Fanelli F., Ferré N., Filiba O., Pedraza-González L., González R., González-Espinoza C. E., Kar R. K., Kemmler L., Kim S. S., Kongsted J., Krylov A. I., Lahav Y., Lazaratos M., NasserEddin Q., Navizet I., Nemukhin A.V., Olivucci M., Olsen J. M. H., Pérez de Alba Ortíz A., Pieri E., Rao A. G., Rhee Y. M., Ricardi N., Sen S., Solov’yov I. A., De Vico L., Wesolowski T. A., Wiebeler C., Yang X., Schapiro I.
    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., Krylov A.I.
    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., Dvoryak S.V., Dudin A.A., Khvostov V.V.
    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., Varfolomeev S.D.
    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., Gainullin I.K., Makarov A.A.
    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., Millionshchikov D.V.
    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
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