72. Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling., Gusev F, Gutkin E, Kurnikova MG, Isayev O., J. Chem. Inf. Model. 63(2) pp 583-594, (2023)

71. Protein-Ligand Binding Free-Energy Calculations with ARROW─A purely first-principles parameterized polarizable force field. Nawrocki G, Leontyev I, Sakipov S, Darkhovskiy M, Kurnikov I, Pereyaslavets L, Kamath G, Voronina E, Butin O, Illarionov A, Olevanov M, Kostikov A, Ivahnenko I, Patel DS, Sankaranarayanan SKRS, Kurnikova MG, Lock C, Crooks GE, Levitt M, Kornberg RD, Fain B., J .Chem. Theory Comput. 18(12) pp7751-7763 (2022)

70. Inhibition of NMDA receptors through a membrane-to-channel path. Wilcox MR, Nigam A, Glasgow NG, Narangoda C, Phillips MB, Patel DS, Mesbahi-Vasey S, Turcu AL, Vázquez S, Kurnikova MG, Johnson JW., Nat Commun. 13(1) pp 4114 (2022)

69. Design, synthesis, and in vitro and in vivo characterization of new memantine analogs for Alzheimer's disease. Turcu AL, Companys-Alemany J, Phillips MB, Patel DS, Griñán-Ferré C, Loza MI, Brea JM, Pérez B, Soto D, Sureda FX, Kurnikova MG, Johnson JW, Pallàs M, Vázquez S., Eur. J. Med. Chem. 236:114354 (2022)

68. Opening of glutamate receptor channel to subconductance levels. Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI., Nature 605(7908), pp 172-178 (2022)

67. Structural mechanism of TRPM7 channel regulation by intracellular magnesium. Schmidt E, Narangoda C, Nörenberg W, Egawa M, Rössig A, Leonhardt M, Schaefer M, Zierler S, Kurnikova MG, Gudermann T, Chubanov V., Cell Mol Life Sci. 79(5) pp 225 (2022)

66. Accurate determination of solvation free energies of neutral organic compounds from first principles. Pereyaslavets L, Kamath G, Butin O, Illarionov A, Olevanov M, Kurnikov I, Sakipov S, Leontyev I, Voronina E, Gannon T, Nawrocki G, Darkhovskiy M, Ivahnenko I, Kostikov A, Scaranto J, Kurnikova MG, Banik S, Chan H, Sternberg MG, Sankaranarayanan SKRS, Crawford B, Potoff J, Levitt M, Kornberg RD, Fain B., Nat Commun., 13(1), pp 414 (2022)

65. Structural basis of AMPA receptor inhibition by trans-4-butylcyclohexane carboxylic acid. Yelshanskaya MV, Singh AK, Narangoda C, Williams RSB, Kurnikova MG, Sobolevsky AI, Br J Pharmacol. (2022) 179(14), pp 3628-3644, Epub 2020

64. Baseline Comparisons of Complementary sampling methods for assembly driven by short-ranged pair potentials toward fast and flexible hybridization. Ozkan A, Sitharam M, Flores-Canales JC, Prabhu R, Kurnikova M.,J. Chem. Theory Comput. 17(3) pp 1967-1987 (2021)

63. Structure and function of the calcium-selective TRP channel TRPV6. Yelshanskaya MV, Nadezhdin KD, Kurnikova MG, Sobolevsky AI., J. Physiol. 599(10) pp 2673-2697 (2021)

62. Harnessing the substrate promiscuity of dioxygenase AsqJ and developing efficient chemoenzymatic synthesis for quinolones. Tang H, Tang Y, Kurnikov IV, Liao HJ, Chan NL, Kurnikova MG, Guo Y, Chang WC., ACS Catal. 11(12) pp 7186-7192 (2021)

61. Epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent oxygenase, AsqJ: Mechanistic elucidation of oxygen atom transfer by a ferryl intermediate. Li J, Liao HJ, Tang Y, Huang JL, Cha L, Lin TS, Lee JL, Kurnikov IV, Kurnikova MG, Chang WC, Chan NL, Guo Y., J Am Chem Soc.142(13) pp 6268-6284 (2020)

60. AMPA receptor noncompetitive inhibitors occupy a promiscuous binding site. Narangoda C, Sakipov SN, Kurnikova MG., ACS Chem. Neurosci. 10(11) pp 4511-4521 (2019)

59.  A Hierarchical Approach to Predict Conformation Dependent Histidine Protonation States in Stable and Flexible Proteins., Sakipov SN., Flores-Canales JC., Kurnikova MG., J. Phys. Chem. B, 123(24), pp 5024-5034 (2019)

58.  Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution, Flores-Canales JC., Simakov NA., Kurnikova MG., bioRxiv 572040, doi: https://doi.org/10.1101/572040 (2018)

57. Sakipov S, Sobolevsky AI, Kurnikova MG. Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6. Sci Rep. 8(1):5715. (2018)

56. Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL, Chang WC. Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation. Angew Chem Int Ed Engl. ;57(7):1831-1835. doi: 10.1002/anie.201710567 (2018)

55. Simakov NA, Kurnikova MG. Membrane Position Dependency of the pKa and Conductivity of the Protein Ion Channel. J Membr Biol. doi: 10.1007/s00232-018-0013-3. (2018)

54. Khan S, Farooq U, Kurnikova M. Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation. Mol Biosyst. 13(9):1874-1887. (2017)

53. Yelshanskaya MV, Mesbahi-Vasey S, Kurnikova MG, Sobolevsky AI. Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating. Sci Rep. 7(1):1050.  (2017

52. Mesbahi-Vasey S, Veras L, Yonkunas M, Johnson JW, Kurnikova MG. All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water. PLoS One. 12(6):e0177686. (2017)

51. Yonkunas M., Buddhadev M., Flores Canales J.C., Kurnikova M., Configurational preference of the glutamate receptor ligand binding domain dimers, Biophys. J., 112(11):2291-2300.(2017)

50. Sakipov, S; Rafikova, O; Kurnikova, MG; Rafikov, R. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobinRedox Biology , 11, 516-523 (2017)

49. Yelshanskaya M.V. , Singh A.K., Sampson J.M., Narangoda C., Kurnikova M., Sobolevsky A.I., Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs, Neuron, 91(6), pp. 1305–1315 (2016)

48. Khan S, Farooq U, Kurnikova M. Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins. J Chem Inf Model. 56(11):2129-2139. Epub 2016 Oct 14. (2016)

47. Flores-Canales J. and Kurnikova M., Microsecond simulations of the diphtheria toxin translocation domain in association with anionic lipid bilayersJ. Phys. Chem B, 119(36), pp 12074-12085 (2015

46. Yonkunas M. and Kurnikova M., The hydrophobic effect contributes to the closed state of a simplified ion channel through a conserved hydrophobic patch at the pore-helix crossing. Frontiers of Pharmacology (Front Pharmacol), 6, pp 284 (2015)

45. Kurnikov I. and Kurnikova M., Modeling electronic polarizability changes in the course of water ligand exchange around magnesium. J. Phys. Chem B, Vol 119 (32), pp 10275- 10286 (2015)

44. Gathak C., Rodnin M.V., Vargas-Uribe M., McCluskey A.J., Flores-Canales J.C., Kurnikova M., Ladokhin A.S., Role of Acidic Residues in Helices TH8-TH9 in Membrane Interactions of the Diphtheria Toxin T domain, Toxins, Vol 7 (4), pp 1303-1323 (2015)

43. Flores-Canales J., Vargas M., Ladokhin A. and Kurnikova M., Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment, J. Membr. Biol., 248 (3), pp 529-543 (2015)

42. Flores-Canales J. and Kurnikova M., Targeting Direct-Space Intra-Solute Electrostatic Interactions in Accelerated Molecular Dynamics with Application to Protein Partial UnfoldingJournal of Chemical Theory and Computation , 11 (6), pp 2550-2559 (2015)

41. Liu Z, Szarecka A, Yonkunas M, Speranskiy K, Kurnikova M, Cascio M., Crosslinking constraints and computational models as complementary tools in modeling the extracellular domain of the glycine receptor. PLoS One.9(7):e102571. (2014)

40. Simakov N.A., Kurnikova M.G., Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels. Molecular Based Mathematical Biology Vol 1, pp 151-163 (2013)

39. Kurnikov I.V., Kyrychenko A., Flores-Canales J.C., Rodnin M.V., Simakov N., Vargas- Uribe M., Posokhov Y.O., Kurnikova M., and Ladokhin A.S., pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines. J. Molecular Biology Vol 425 (15), pp2752-64 (2013)

38. Mamonova T., Glyakina A.V., Galzitskaya O.V., Kurnikova M.G., Stability and rigidity/flexibility—Two sides of the same coin? Biochimica et Biophysica Acta, 1834 (2013), 854–866 (2013)

37. Mamonova T., Kurnikova M., and Friedman P.A., Structural Basis for NHERF1 PDZ Domain Binding. Biochemistry, 51 (14), 3110–3120 (2012)

36. Yonkunas M. and Kurnikova M., Characterizing the Energetic States of the GluR2 Ligand Binding Domain Core-Dimer. Biophys. J., 100(2), L5-L7 (2011)

35. Simakov N. and Kurnikova K., Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin. J. Phys. Chem. B, 114(46), 15180-15190 (2010)

34. Mamonova T.B., Glyakina A.V., Kurnikova M.G. and Galzitskaya O.G., Flexibility and Mobility in Mesophilic and Thermophilic Homologous Proteins from Molecular Dynamics and FoldUnfold Method. J. Bioinform. and Comp. Biol., 8(3), 377-394 (2010)

33. Ramanathan A., Agarwal P. K., Kurnikova M., Langmead C.J. An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations J. Comp. Biol.,17 (3), 309-324 (2010) (invited submission)

32. Ramanathan A., Agarwal P. K., Kurnikova M., Langmead C.J. An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 138-154 (2009)

31. Ramanathan A., Mamonova T., Madrid M., Kurnikova M. Biologically Relevant Motions of HIV-1 Reverse Transcriptase Investigated by Long-scale Molecular Dynamics, Proceedings of the 3rd Annual TeraGrid conference. (2009)

30. Speranskiy K. and Kurnikova M. Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor. Prot. Struct. Func. Bioinf.,76 (2): 271-280 (2009)

29. Liu Z., Ramanoudjame G., Fox R., Jayaraman V., Kurnikova M. and Cascio M. Overexpression and functional characterization of the extracellular domain of the human α1 glycine receptor, Biochemistry 47: 9803-9810 (2008)

28. Mamonova T., Yonkunas M. and Kurnikova M. Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain, Biochemistry, 47 (42): 11077-11085 (2008)

27. Kurnikova M. Ion Channels, Computation of; in Wiley Encyclopedia of Chemical Biology, ed. Tadhg P. Begley, Wiley, ISBN: 978-0- 471-75477- 0 (2008)

26. Cheng M.H. , Coalson R.D., Cascio M., and Kurnikova M. Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds J. Comput. Aided Mol. Des. 22: 563-570 (2008)

25. Mamonova T., Speranskiy K., and Kurnikova M. Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2. Prot. Struct. Func. Bioinf., 73(3): 656-671 (2008)

24. Widge A., Matsuoka Y., Kurnikova M. Replica Exchange Molecular Dynamics Simulation of Poly(alkylthiophenes) J. Mol. Graph. Comput. 27: 34-44 (2008)

23. Widge A., Matsuoka Y., Kurnikova M., Computational Modeling of Poly(alkylthiophene) Conductive Polymer Insertion Into Phospholipid Bilayers, Langmuir 23: 10672-10681 (2007)

22. Speranskiy K., Casio M., Kurnikova M., Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain, Prot. Struct. Func. Bioinf. 67(4): 950-960 (2007)

21. Coalson R.D. and Kurnikova M.G., Poisson-Nernst- Planck theory of ion permeation through biological channels”, in: Biological Membrane Ion Channels. Dynamics, Structure, and Applications, S-H Chung, O. Andersen and V. Krishnamurthy, Ed. Springer Verlag, (2006).

20. Mamonov A., Kurnikova M., Coalson R., Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods, Biophys. Chem. 124(3): 268-278 (2006)

19. Mamonova T. and Kurnikova M., Structure and energetics of channel-forming protein- polysaccharide complexes inferred via computational statistical thermodynamics. J.Phys.Chem. 110(49): 25091-25100 (2006)

18. Karnup S. V., Hayar A., Shipley M. T., Kurnikova M.G., Spontaneous field potentials in the glomeruli of the olfactory bulb: The leading role of juxtaglomerular cells, Neuroscience 142 (1): 203-221 (2006)

17. Mamonova T., Hespenheide B., Straub R., Thorpe M. and Kurnikova M., Protein Flexibility using Constraints from Molecular Dynamics Simulations Phys. Biol. 2 S137- S147 (2005)

16. Speranskiy K. and Kurnikova M., Investigation of the glutamate ligand binding to the Glutamate Receptor by theoretical methodologies, Biochemistry 44(34) 11508-11517 (2005)

15. Coalson R.D. and Kurnikova M.G., Poisson-Nernst- Planck theory approach to the calculation of current through biological ion channels. IEEE Transaction on NanoBioscience 4(1) 81-93 (2005)

14. Speranskiy K. and Kurnikova M., Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form. J. Chem. Phys. 121 1516-1524 (2004)

13. Graf P., Kurnikova M.G., Coalson R.D. and Nitzan A., Comparison of dynamic lattice Monte Carlo simulations and the dielectric self-energy Poisson-Nernst- Planck continuum theory for model ion channels. J. Phys. Chem. 108 2006-2015 (2004)

12. Shilov I. and Kurnikova M., Energetics and dynamics of a cyclic oligosaccharide molecule in a confined protein pore environment. A molecular dynamics study. J.Phys.Chem. 107(29) 71089-7201 (2003)

11. Mamonov A., Coalson R., Nitzan A. and Kurnikova M., The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single channel currents. Biophys. J., 84(6), 3646-3661 (2003)

10. Graf P., Nitzan A., Kurnikova M.G. and Coalson R.D., A dynamic lattice Monte-Carlo model of ion transport in inhomogeneous dielectric environments: method and implementation. J.Phys.Chem., 104, 12324-12338 (2000)

9. Cardenas A., Kurnikova M. and Coalson R., 3D Poisson-Nernst- Planck theory studies of the influence of membrane electrostatics on Gramicidin A channel conductance. Biophys. J., 79, 80-93 (2000)

8. Kurnikova M.G., Coalson R.D., Graf P. and Nitzan A., A lattice relaxation algorithm for 3D Poisson-Nernst- Planck theory with application to ion transport through the Gramicidin A channel. Biophys. J., 76, 642-656 (1999)

7. Balabai N., Sukharevsky A., Read I., Strazisar B., Kurnikova M., Hartman R.S., Coalson R.D. and Waldeck D.H., Rotational diffusion of organic solutes: the role of dielectric friction in polar solvents and electrolyte solutions. J. Mol. Liquids, 77, 37-60 (1998)

6. Balabai N., Kurnikova M.G., Coalson R.D. and Waldeck D.H., Rotational relaxation of ionic molecules in electrolyte solutions. Anisotropy relaxation and molecular dynamics study. J. Am. Chem. Soc., 120(31), 7944-7951 (1998)

5. Kurnikova M.G., Balabai N., Waldeck D.H. and Coalson R.D. Rotational relaxation in polar solvents. Molecular dynamics study of solute-solvent interactions. J. Am. Chem. Soc., 120(24), 6121-6130 (1998)

4. Kurnikov I.V., Zusman L.D., Kurnikova M.G., Farid R.S. and Beratan D.N., Structural fluctuations, spin, reorganization energy, and tunneling energy control of intramolecular electron transfer: The surprising case of electron transfer in a d8-d8 bimetallic system. J. Am. Chem. Soc., 119(24), 5690-5700 (1997)

3. Zahorchak J.C., Kurnikova M.G., and Coalson R.D., A Molecular dynamics study of photothermal compression of colloidal crystals. J. Chem. Phys., 105(23), 628-638 (1996)

2. Kurnikova M.G., Waldeck D.H. and Coalson R.D. A Molecular dynamics study of dielectric friction. J. Chem. Phys., 105(2), 628-638 (1996)

1. Bacharev B.V. and Kurnikova M.G., Methods of the statistical analysis of the EEG data. Software package for the personal computer Iskra. Russian Academy of Science, Pushchino (1991)