| 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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