Maria G Kurnikova, Ph.D. - Publications

Affiliations: 
2003- chemistry Carnegie Mellon University, Pittsburgh, PA 
Area:
computational chemistry and biochemistry, structural biophysics, structure-function relationaships in proteins, AMPA, NMDA, ion channels

101 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Gutkin E, Gusev F, Gentile F, Ban F, Koby SB, Narangoda C, Isayev O, Cherkasov A, Kurnikova MG. screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations. Chemical Science. 15: 8800-8812. PMID 38873063 DOI: 10.1039/d3sc06880c  0.611
2024 Gangwar SP, Yelshanskaya MV, Nadezhdin KD, Yen LY, Newton TP, Aktolun M, Kurnikova MG, Sobolevsky AI. Kainate receptor channel opening and gating mechanism. Nature. PMID 38778115 DOI: 10.1038/s41586-024-07475-0  0.76
2024 Nadezhdin KD, Correia L, Shalygin A, Aktolun M, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI. Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930. Cell Reports. 43: 114108. PMID 38615321 DOI: 10.1016/j.celrep.2024.114108  0.755
2023 Khoreva A, Butov KR, Nikolaeva EI, Martyanov A, Kulakovskaya E, Pershin D, Alexenko M, Kurnikova M, Abasov R, Raykina E, Abramov D, Arnaudova K, Rodina Y, Trubina N, Skvortsova Y, et al. Novel hemizygous variant leads to combined immunodeficiency with defective platelet calcium signaling and cell mobility. The Journal of Allergy and Clinical Immunology. Global. 3: 100172. PMID 37915722 DOI: 10.1016/j.jacig.2023.100172  0.553
2023 Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Kamath G, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, ... ... Kurnikova MG, et al. Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions. Journal of the American Chemical Society. 145: 23620-23629. PMID 37856313 DOI: 10.1021/jacs.3c07628  0.785
2023 Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, et al. A community effort in SARS-CoV-2 drug discovery. Molecular Informatics. PMID 37833243 DOI: 10.1002/minf.202300262  0.583
2023 Nadezhdin KD, Correia L, Narangoda C, Patel DS, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI. Structural mechanisms of TRPM7 activation and inhibition. Nature Communications. 14: 2639. PMID 37156763 DOI: 10.1038/s41467-023-38362-3  0.759
2023 Chen L, Mamutova A, Kozlova A, Latysheva E, Evgeny F, Latysheva T, Savostyanov K, Pushkov A, Zhanin I, Raykina E, Kurnikova M, Mersiyanova I, Platt CD, Jee H, Brodeur K, et al. Comparison of disease phenotypes and mechanistic insight on causal variants in patients with DADA2. The Journal of Allergy and Clinical Immunology. PMID 37150360 DOI: 10.1016/j.jaci.2023.04.014  0.539
2023 Gusev F, Gutkin E, Kurnikova MG, Isayev O. Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. Journal of Chemical Information and Modeling. PMID 36599125 DOI: 10.1021/acs.jcim.2c01052  0.611
2022 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, et al. Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field. Journal of Chemical Theory and Computation. PMID 36459593 DOI: 10.1021/acs.jctc.2c00930  0.8
2022 Wilcox MR, Nigam A, Glasgow NG, Narangoda C, Phillips MB, Patel DS, Mesbahi-Vasey S, Turcu AL, Vázquez S, Kurnikova MG, Johnson JW. Inhibition of NMDA receptors through a membrane-to-channel path. Nature Communications. 13: 4114. PMID 35840593 DOI: 10.1038/s41467-022-31817-z  0.705
2022 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. Design, synthesis, and in vitro and in vivo characterization of new memantine analogs for Alzheimer's disease. European Journal of Medicinal Chemistry. 236: 114354. PMID 35453065 DOI: 10.1016/j.ejmech.2022.114354  0.649
2022 Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI. Opening of glutamate receptor channel to subconductance levels. Nature. 605: 172-178. PMID 35444281 DOI: 10.1038/s41586-022-04637-w  0.761
2022 Schmidt E, Narangoda C, Nörenberg W, Egawa M, Rössig A, Leonhardt M, Schaefer M, Zierler S, Kurnikova MG, Gudermann T, Chubanov V. Structural mechanism of TRPM7 channel regulation by intracellular magnesium. Cellular and Molecular Life Sciences : Cmls. 79: 225. PMID 35389104 DOI: 10.1007/s00018-022-04192-7  0.634
2022 Fedorova D, Ovsyannikova G, Kurnikova M, Pavlova A, Konyukhova T, Pshonkin A, Smetanina N. De novo TP53 germline activating mutations in two patients with the phenotype mimicking Diamond-Blackfan anemia. Pediatric Blood & Cancer. 69: e29558. PMID 35084091 DOI: 10.1002/pbc.29558  0.528
2022 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, et al. Accurate determination of solvation free energies of neutral organic compounds from first principles. Nature Communications. 13: 414. PMID 35058472 DOI: 10.1038/s41467-022-28041-0  0.79
2021 Tang H, Tang Y, Kurnikov IV, Liao HJ, Chan NL, Kurnikova MG, Guo Y, Chang WC. Harnessing the Substrate Promiscuity of Dioxygenase AsqJ and Developing Efficient Chemoenzymatic Synthesis for Quinolones. Acs Catalysis. 11: 7186-7192. PMID 35721870 DOI: 10.1021/acscatal.1c01150  0.545
2021 Ozkan A, Sitharam M, Flores-Canales JC, Prabhu R, Kurnikova M. Baseline Comparisons of Complementary Sampling Methods for Assembly Driven by Short-Ranged Pair Potentials toward Fast and Flexible Hybridization. Journal of Chemical Theory and Computation. PMID 33576635 DOI: 10.1021/acs.jctc.0c00945  0.73
2020 Yelshanskaya MV, Singh AK, Narangoda C, Williams RSB, Kurnikova MG, Sobolevsky AI. Structural basis of AMPA receptor inhibition by 4-BCCA. British Journal of Pharmacology. PMID 32959886 DOI: 10.1111/Bph.15254  0.735
2020 Li J, Liao HJ, Tang Y, Huang JL, Cha L, Lin TS, Lee JL, Kurnikov IV, Kurnikova MG, Chang WC, Chan NL, Guo Y. Epoxidation Catalyzed by the Non-heme Iron- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate. Journal of the American Chemical Society. PMID 32131594 DOI: 10.1021/Jacs.0C00484  0.608
2020 Yelshanskaya MV, Nadezhdin KD, Kurnikova MG, Sobolevsky AI. Structure and function of the calcium-selective TRP channel TRPV6. The Journal of Physiology. PMID 32073143 DOI: 10.1113/Jp279024  0.775
2020 Kurnikova MG, Sakipov S, Kottke C, Narangoda C, Scaranto J. Dynamical Mechanisms of Glutamate Receptor Gating and Sub-Conductance Biophysical Journal. 118: 581a. DOI: 10.1016/J.Bpj.2019.11.3151  0.764
2019 Narangoda C, Sakipov SN, Kurnikova MG. AMPA Receptor Noncompetitive Inhibitors Occupy a Promiscuous Binding Site. Acs Chemical Neuroscience. PMID 31596070 DOI: 10.1021/Acschemneuro.9B00344  0.798
2019 Sakipov SN, Flores-Canales JC, Kurnikova MG. A Hierarchical Approach to Predict Conformation Dependent Histidine Protonation States in Stable and Flexible Proteins. The Journal of Physical Chemistry. B. PMID 31095377 DOI: 10.1021/Acs.Jpcb.9B00656  0.794
2019 Sakipov S, Narangoda Cm, Mesbahi S, Flores-Canales JC, Kottke C, Kurnikova MG. Agonist and Inhibitor Binding Effects on AMPA Receptor Internal Structure and Dynamics Biophysical Journal. 116: 107a. DOI: 10.1016/J.Bpj.2018.11.611  0.771
2019 Narangoda C, Sakipov S, Kurnikova MG. Computational Characterization of the Binding of Non-Competitive Inhibitors to AMPA Receptors Biophysical Journal. 116: 106a-107a. DOI: 10.1016/J.Bpj.2018.11.609  0.761
2019 Kurnikova MG. After the Structure Comes the Dynamics: Molecular Modeling of Glutamate Receptors Reveals Long-Range Allosteric Coupling between Ligand Binding Site and Channel Gate Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.170  0.418
2018 Sakipov S, Sobolevsky AI, Kurnikova MG. Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6. Scientific Reports. 8: 5715. PMID 29632318 DOI: 10.1038/S41598-018-23972-5  0.794
2018 Simakov NA, Kurnikova MG. Membrane Position Dependency of the pKa and Conductivity of the Protein Ion Channel. The Journal of Membrane Biology. PMID 29340712 DOI: 10.1007/S00232-018-0013-3  0.806
2018 Chang WC, Liao HJ, Li J, Huang JL, Davidson M, Kurnikov I, Lin TS, Lee JL, Kurnikova M, Guo Y, Chan NL. Insights into desaturation of cyclopeptin and its C3-epimer catalyzed by a non-heme iron enzyme: structural characterization and mechanism elucidation. Angewandte Chemie (International Ed. in English). PMID 29314482 DOI: 10.2210/Pdb5Y7T/Pdb  0.59
2017 Khan S, Farooq U, Kurnikova M. Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation. Molecular Biosystems. PMID 28737816 DOI: 10.1039/C7Mb00210F  0.652
2017 Yonkunas M, Buddhadev M, Flores Canales JC, Kurnikova MG. Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers. Biophysical Journal. 112: 2291-2300. PMID 28591602 DOI: 10.1016/J.Bpj.2017.04.042  0.687
2017 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: e0177686. PMID 28582391 DOI: 10.1371/Journal.Pone.0177686  0.758
2017 Yelshanskaya MV, Mesbahi-Vasey S, Kurnikova MG, Sobolevsky AI. Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating. Scientific Reports. 7: 1050. PMID 28432359 DOI: 10.1038/S41598-017-01146-Z  0.789
2017 Sakipov S, Rafikova O, Kurnikova MG, Rafikov R. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin. Redox Biology. 11: 516-523. PMID 28088643 DOI: 10.1016/J.Redox.2017.01.004  0.782
2017 Sakipov S, Sobolevsky AI, Kurnikova M. Ion Permeation Mechanism in TRPV6 Ca 2+ Channel Biophysical Journal. 112: 466a. DOI: 10.1016/J.Bpj.2016.11.2498  0.797
2017 Sayede Mesbahi S, Johnson JW, Kurnikova M. Modeling Ion Selectivity in Transmembrane Domain of the NMDA Receptor Biophysical Journal. 112: 423a. DOI: 10.1016/J.Bpj.2016.11.2262  0.707
2016 Khan S, Farooq U, Kurnikova M. Exploring Protein Stability by Comparative Molecular Dynamics Simulation of Homologous Hyperthermophilic, Mesophilic and Psychrophilic Proteins. Journal of Chemical Information and Modeling. PMID 27668309 DOI: 10.1021/Acs.Jcim.6B00305  0.629
2016 Yelshanskaya MV, Singh AK, Sampson JM, Narangoda C, Kurnikova M, Sobolevsky AI. Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs. Neuron. PMID 27618672 DOI: 10.1016/J.Neuron.2016.08.012  0.773
2016 Kurnikova M. Will it Permeate? Predicting Ion Channel Ion Selectivity, Permittivity and Block Mechanisms Biophysical Journal. 110: 376. DOI: 10.1016/J.Bpj.2015.11.2029  0.683
2015 Yonkunas M, 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 in Pharmacology. 6: 284. PMID 26640439 DOI: 10.3389/Fphar.2015.00284  0.701
2015 Flores-Canales JC, Kurnikova M. Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding. Journal of Chemical Theory and Computation. 11: 2550-9. PMID 26575554 DOI: 10.1021/Ct501090Y  0.67
2015 Flores-Canales JC, Kurnikova M. Microsecond Simulations of the Diphtheria Toxin Translocation Domain in Association with Anionic Lipid Bilayers. The Journal of Physical Chemistry. B. 119: 12074-85. PMID 26305016 DOI: 10.1021/Acs.Jpcb.5B07909  0.656
2015 Kurnikov IV, Kurnikova M. Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process. The Journal of Physical Chemistry. B. 119: 10275-86. PMID 26109375 DOI: 10.1021/Acs.Jpcb.5B01295  0.648
2015 Ghatak C, Rodnin MV, Vargas-Uribe M, McCluskey AJ, Flores-Canales JC, Kurnikova M, Ladokhin AS. Role of acidic residues in helices TH8-TH9 in membrane interactions of the diphtheria toxin T domain. Toxins. 7: 1303-23. PMID 25875295 DOI: 10.3390/Toxins7041303  0.634
2015 Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, Kurnikova M. Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. The Journal of Membrane Biology. 248: 529-43. PMID 25650178 DOI: 10.1007/S00232-015-9771-3  0.643
2015 Sakipov S, Kurnikova M, Rafikov R. Bio-Catalysis of Heme Extraction from Extracellular Hemoglobin for Sickle Cell Disease and Hemolysis Treatment Free Radical Biology and Medicine. 87: S56. DOI: 10.1016/J.Freeradbiomed.2015.10.146  0.746
2015 Mesbahi S, Veras L, Johnson JW, Kurnikova M. NMDA Receptor Transmembrane Domain: Structure and Mechanism of Ion Selectivity Biophysical Journal. 108: 384a. DOI: 10.1016/J.Bpj.2014.11.2107  0.753
2014 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: e102571. PMID 25025226 DOI: 10.1371/Journal.Pone.0102571  0.675
2014 Yonkunas M, Buddhadev M, Kurnikova M. Characterizing the Energetic States of a Glutamate Receptor using Umbrella Sampling and Microsecond Molecular Dynamics Simulations Biophysical Journal. 106: 152a. DOI: 10.1016/J.Bpj.2013.11.873  0.677
2014 Flores-Canales JC, Ladokhin AS, Kurnikova M. Multiscale Simulations of Diphtheria Toxin T-Domain Membrane Association Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.2484  0.647
2013 Kurnikov IV, Kyrychenko A, Flores-Canales JC, Rodnin MV, Simakov N, Vargas-Uribe M, Posokhov YO, Kurnikova M, Ladokhin AS. pH-triggered conformational switching of the diphtheria toxin T-domain: the roles of N-terminal histidines. Journal of Molecular Biology. 425: 2752-64. PMID 23648837 DOI: 10.1016/J.Jmb.2013.04.030  0.796
2013 Mamonova TB, Glyakina AV, Galzitskaya OV, Kurnikova MG. Stability and rigidity/flexibility-two sides of the same coin? Biochimica Et Biophysica Acta. 1834: 854-66. PMID 23416444 DOI: 10.1016/J.Bbapap.2013.02.011  0.638
2013 Simakov NA, Kurnikova MG. Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels Computational and Mathematical Biophysics. 1: 151-163. DOI: 10.2478/Mlbmb-2013-0008  0.777
2013 Abroshan H, Yonkunas M, Johnson JW, Kurnikova M. Glutamate Receptor Model and Atomistic Simulations; AMPA and NMDA Biophysical Journal. 104: 271a. DOI: 10.1016/J.Bpj.2012.11.1522  0.747
2013 Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, Kurnikova M. Membrane Association of Diphtheria Toxin T-Domain Characterized by Coarse-Grained and Atomistic Molecular Dynamics Simulations and Experiments Biophysical Journal. 104: 2-8. DOI: 10.1016/J.Bpj.2012.11.1345  0.662
2012 Mamonova T, Kurnikova M, Friedman PA. Structural basis for NHERF1 PDZ domain binding. Biochemistry. 51: 3110-20. PMID 22429102 DOI: 10.1021/Bi201213W  0.664
2012 Veras L, Kurnikov I, Johnson JW, Kurnikova M. Computational Studies of the Molecular Mechanisms Responsible for Ca2+ Permeation and Mg2+ Block of NMDA Receptors Biophysical Journal. 102: 612a-613a. DOI: 10.1016/J.Bpj.2011.11.3340  0.747
2012 Flores JC, Kurnikov I, Kurnikova M. An Empirical Scoring Function for the Transmembrane Helical Protein Assembly Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2576  0.66
2011 Kurnikova M, Maschan M, Dinova E, Shagina I, Finogenova N, Mamedova E, Polovtseva T, Shagin D, Shcherbina A. Four novel ELANE mutations in patients with congenital neutropenia. Pediatric Blood & Cancer. 57: 332-5. PMID 21425445 DOI: 10.1002/pbc.23104  0.525
2011 Kurnikova M, Dinova E, Shagina I, Shagin D. Alu-mediated recombination in the HAX1 gene as the molecular basis of severe congenital neutropenia. American Journal of Medical Genetics. Part A. 155: 660-1. PMID 21344642 DOI: 10.1002/ajmg.a.33893  0.545
2011 Yonkunas M, Kurnikova M. Characterizing the energetic states of the GluR2 ligand binding domain core-dimer. Biophysical Journal. 100: L5-7. PMID 21244821 DOI: 10.1016/J.Bpj.2010.10.048  0.663
2011 Yonkunas MJ, Kurnikova M. A Hydrophobic Bundle Crossing Found in Glutamate Receptor and K+ channel Pore Helices Dominates the Conformational Free Energy Landscape Biophysical Journal. 100: 24a. DOI: 10.1016/J.Bpj.2010.12.339  0.676
2011 Veras L, Younkunas M, Hwang J, Kallenbach E, Kurnikov I, Johnson JW, Kurnikova M. Molecular Mechanisms of Ca2+ Selectivity and Mg2+ Block of NMDA Receptors Biophysical Journal. 100: 269a. DOI: 10.1016/J.Bpj.2010.12.1680  0.751
2011 Flores-Canales JC, Kurnikov I, Simakov N, Kyrychenko A, Rodnin MV, Ladokhin AS, Kurnikova M. Mechanism of the pH-Triggered Formation of Membrane-Competent State of the Diphtheria Toxin Translocation Domain Revealed by Simulations and Experiment Biophysical Journal. 100: 206a. DOI: 10.1016/J.Bpj.2010.12.1336  0.794
2010 Simakov NA, Kurnikova MG. Soft wall ion channel in continuum representation with application to modeling ion currents in α-hemolysin. The Journal of Physical Chemistry. B. 114: 15180-90. PMID 21028776 DOI: 10.1021/Jp1046062  0.813
2010 Mamonova TB, Glyakina AV, Kurnikova MG, Galzitskaya OV. Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method. Journal of Bioinformatics and Computational Biology. 8: 377-94. PMID 20556851 DOI: 10.1142/S0219720010004690  0.653
2010 Ramanathan A, Agarwal PK, Kurnikova M, Langmead CJ. An online approach for mining collective behaviors from molecular dynamics simulations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 309-24. PMID 20377447 DOI: 10.1089/Cmb.2009.0167  0.628
2010 Mamonova T, Wang B, Kurnikova M, Friedman PA. Modeling and Mutation of NHERF1 Dimerization Domains Biophysical Journal. 98: 58a. DOI: 10.1016/J.Bpj.2009.12.332  0.646
2010 Yonkunas MJ, Kurnikova M. Theoretical Investigation of Structure and Gating Mechanisms in Glutamate Receptor Ion Channels Biophysical Journal. 98: 524a. DOI: 10.1016/J.Bpj.2009.12.2849  0.71
2010 Simakov NA, Kurnikova MG. Extension of Poisson-Nernst Planck Theory of Ion Conductivity with Soft-Repulsion Potential between Ions and Protein. Sensitivity of I-V Properties of α-Hemolysin Channel on its Penetration Depth into Membrane Biophysical Journal. 98: 333a. DOI: 10.1016/J.Bpj.2009.12.1808  0.789
2009 Speranskiy K, Kurnikova MG. Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor. Proteins. 76: 271-80. PMID 19205024 DOI: 10.1002/Prot.22332  0.681
2009 Kurnikova M, Shagina I, Khachatryan L, Schagina O, Maschan M, Shagin D. Identification of a novel mutation in DKC1 in dyskeratosis congenita. Pediatric Blood & Cancer. 52: 135-7. PMID 18802941 DOI: 10.1002/pbc.21733  0.527
2009 Simakov NA, Kurnikova MG. Calculation of Current-Voltage properties of Biological Ion Channel, using Poisson-Nernst-Planck (PNP) Theory Biophysical Journal. 96: 662a. DOI: 10.1016/J.Bpj.2008.12.3498  0.798
2009 Farrell DW, Mamonova T, Kurnikova M, Thorpe MF. Generating Pathways for Free Energy Calculations in Proteins Using Constraint-Based Conformational Sampling Biophysical Journal. 96: 407a. DOI: 10.1016/J.Bpj.2008.12.2072  0.655
2008 Mamonova T, Yonkunas MJ, Kurnikova MG. Energetics of the cleft closing transition and the role of electrostatic interactions in conformational rearrangements of the glutamate receptor ligand binding domain. Biochemistry. 47: 11077-85. PMID 18823129 DOI: 10.1016/J.Bpj.2008.12.2534  0.687
2008 Liu Z, Ramanoudjame G, Liu D, Fox RO, Jayaraman V, Kurnikova M, Cascio M. Overexpression and functional characterization of the extracellular domain of the human alpha1 glycine receptor. Biochemistry. 47: 9803-10. PMID 18710260 DOI: 10.1021/Bi800659X  0.658
2008 Mamonova T, Speranskiy K, Kurnikova M. Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2. Proteins. 73: 656-71. PMID 18491377 DOI: 10.1002/Prot.22090  0.679
2008 Widge AS, Matsuoka Y, Kurnikova M. Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes). Journal of Molecular Graphics & Modelling. 27: 34-44. PMID 18485769 DOI: 10.1016/J.Jmgm.2008.02.005  0.611
2008 Cheng MH, Coalson RD, Cascio M, Kurnikova M. Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. Journal of Computer-Aided Molecular Design. 22: 563-70. PMID 18368498 DOI: 10.1007/S10822-008-9200-0  0.752
2007 Widge AS, Matsuoka Y, Kurnikova M. Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers. Langmuir : the Acs Journal of Surfaces and Colloids. 23: 10672-81. PMID 17867709 DOI: 10.1021/La070214V  0.626
2007 Speranskiy K, Cascio M, Kurnikova M. Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain. Proteins. 67: 950-60. PMID 17357155 DOI: 10.1002/Prot.21251  0.693
2006 Mamonova T, Kurnikova M. Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics. The Journal of Physical Chemistry. B. 110: 25091-100. PMID 17149934 DOI: 10.1021/Jp065009N  0.647
2006 Karnup SV, Hayar A, Shipley MT, Kurnikova MG. Spontaneous field potentials in the glomeruli of the olfactory bulb: the leading role of juxtaglomerular cells. Neuroscience. 142: 203-21. PMID 16876327 DOI: 10.1016/J.Neuroscience.2006.05.068  0.586
2006 Mamonov AB, Kurnikova MG, Coalson RD. Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods. Biophysical Chemistry. 124: 268-78. PMID 16797116 DOI: 10.1016/J.Bpc.2006.03.019  0.778
2005 Mamonova T, Hespenheide B, Straub R, Thorpe MF, Kurnikova M. Protein flexibility using constraints from molecular dynamics simulations. Physical Biology. 2: S137-47. PMID 16280619 DOI: 10.1088/1478-3975/2/4/S08  0.652
2005 Speranskiy K, Kurnikova M. On the binding determinants of the glutamate agonist with the glutamate receptor ligand binding domain. Biochemistry. 44: 11508-17. PMID 16114887 DOI: 10.1021/Bi050547W  0.67
2005 Coalson RD, Kurnikova MG. Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels. Ieee Transactions On Nanobioscience. 4: 81-93. PMID 15816174 DOI: 10.1109/Tnb.2004.842495  0.746
2004 Speranskiy K, 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. The Journal of Chemical Physics. 121: 1516-24. PMID 15260697 DOI: 10.1063/1.1752887  0.637
2004 Graf P, Kurnikova MG, Coalson RD, Nitzan A. Comparison of Dynamic Lattice Monte Carlo Simulations and the Dielectric Self-Energy Poisson-Nernst-Planck Continuum Theory for Model Ion Channels Journal of Physical Chemistry B. 108: 2006-2015. DOI: 10.1021/Jp0355307  0.799
2003 Mamonov AB, Coalson RD, Nitzan A, Kurnikova MG. The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents. Biophysical Journal. 84: 3646-61. PMID 12770873 DOI: 10.1016/S0006-3495(03)75095-4  0.811
2003 and IYS, Kurnikova MG. Energetics and Dynamics of a Cyclic Oligosaccharide Molecule in a Confined Protein Pore Environment. A Molecular Dynamics Study Journal of Physical Chemistry B. 107: 7189-7201. DOI: 10.1021/Jp034359W  0.401
2000 Cárdenas AE, Coalson RD, Kurnikova MG. Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on gramicidin A channel conductance. Biophysical Journal. 79: 80-93. PMID 10866939 DOI: 10.1016/S0006-3495(00)76275-8  0.798
2000 Graf P, Nitzan A, Kurnikova MG, Coalson RD. A dynamic lattice Monte Carlo model of ion transport in inhomogeneous dielectric environments: Method and implementation Journal of Physical Chemistry B. 104: 12324-12338. DOI: 10.1021/Jp001282S  0.764
1999 Kurnikova MG, Coalson RD, Graf P, Nitzan A. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel. Biophysical Journal. 76: 642-56. PMID 9929470 DOI: 10.1016/S0006-3495(99)77232-2  0.761
1998 Balabai N, Kurnikova MG, Coalson RD, Waldeck DH. Rotational relaxation of ionic molecules in electrolyte solutions. Anisotropy relaxation and molecular dynamics study Journal of the American Chemical Society. 120: 7944-7951. DOI: 10.1021/Ja973393J  0.608
1998 Kurnikova MG, Balabai N, Waldeck DH, Coalson RD. Rotational relaxation in polar solvents. Molecular dynamics study of solute-solvent interaction Journal of the American Chemical Society. 120: 6121-6130. DOI: 10.1021/Ja972926L  0.709
1998 Balabai N, Sukharevsky A, Read I, Strazisar B, Kurnikova M, Hartman R, Coalson R, Waldeck D. Rotational diffusion of organic solutes: the role of dielectric friction in polar solvents and electrolyte solutions Journal of Molecular Liquids. 77: 37-60. DOI: 10.1016/S0167-7322(98)00067-1  0.706
1997 Zahorchak JC, Kurnikova MG, Coalson RD. A molecular dynamics study of photothermal compression of colloidal crystals Journal of Chemical Physics. 106: 1585-1592. DOI: 10.1063/1.473279  0.551
1997 Kurnikov IV, Zusman LD, Kurnikova MG, Farid RS, Beratan DN. 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 Journal of the American Chemical Society. 119: 5690-5700. DOI: 10.1021/Ja970309R  0.687
1996 Kurnikova MG, Waldeck DH, Coalson RD. A molecular dynamics study of dielectric friction The Journal of Chemical Physics. 105: 628-638. DOI: 10.1063/1.471930  0.575
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