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Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels 

N.A. Simakov, M.G. Kurnikova

    Molecular Based Mathematical Biology Vol 1, pp 151-163 (2013) [Link]


pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines  
I.V. Kurnikov, A. Kyrychenko, J.C. Flores-Canales, M.V. Rodnin, N. Simakov, M. Vargas-Uribe, Y.O. Posokhov, M. Kurnikova, and A.S. Ladokhin

    J. Molecular Biology Vol 425 (15), pp2752-64 (2013) 
[Link]


Stability and Rigidity/Flexibility - Two Sides of the Same Coin?
T.Mamonova,
A.Glyakina, O.Galzitskaya, and M.Kurnikova

    BBA - Proteins and Proteomics, Vol 1834, pp 854-866 (2013)  [PDF]


Structural Basis for NERF1 PDZ Domain Binding
   T. Mamonova, M. Kurnikova and P. Friedman
   Biochemistry, Vol 50(14), pp 3110-3120 (2012)
[PDF]


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


Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin
N. Simakov and M. Kurnikova
J. Phys. Chem., Vol. 114(46), pp 15180-15190  (2010) [PDF]


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


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


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


Biologically Relevant Motions of HIV-1 Reverse Transcriptase Investigated by Long-scale Molecular Dynamics
A. Ramathan, T. Mamonova, M. Madrid, M. Kurnikova
Proceedings of the 3rd Annual TeraGrid ’08 conference.(2008) [PDF]


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


Ion Channels, Computational approaches.
M. Kurnikova
in Wiley Encyclopedia of Chemical Biology, ed. T. P. Begley, Wiley, ISBN: 978-0-471-75477-0 (2008)


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


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


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


Computational Prediction of Ion Permeation Characteristics in the Clycine Receptor Modifid by Photo-Sensitive Compounds
M. H. Cheng, R. D. Coalson, M. Cascio, and M. Kurnikova
J. Comput. Aided Mol. Des., Vol. 22, pp. .563-570 (2008) [PDF]


Replica Exchange Molecular Dynamics Simulation of Poly(alkylthiophenes)
A. Widge, Y. Matsuoka, M. Kurnikova
J. Mol. Graph. Model. Vol. 27, pp 34 (2008) [PDF]


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


Homology Model and Molecular Dynamics Simulations of the Glycine Receptor Ligand Binding Domain
K. Sperankiy, M. Casio, M. Kurnikova
Prot.: Struct., Func., Bioinf. Vol 67, pp. 950-960 (2007) [PDF]


Poisson-Nernst-Planck theory of ion permeation through biological channels
R. Coalson, M. Kurnikova
In Book: Biological Membrane Ion Channels. Dynamics, Structure, and Applications (2007)
Ed. S-H Chung, O. Andersen, and V. Krishnamurthy 


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


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


Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics
T. Mamonova, M. G. Kurnikova
J. Phys. Chem., Vol. 110, Iss. 49, pp. 25091-25100 (2006) [PDF]


Protein Flexibility using Constraints from Molecular Dynamics Simulations
T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova
Physical Biology, Vol. 2, S137-S147 (2005) [PDF]


On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain
K. Speranskiy, M. G. Kurnikova
Biochemistry Vol. 44, pp. 11508-11517 (2005) [PDF]


Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels
R. Coalson, M. G. Kurnikova
IEEE Transaction on NanoBioscience Vol. 4, pp. 81-93 (2005) [PDF]


Comparison of Dynamic Lattice Monte Carlo Simulations and the Dielectric Self-Energy Poisson-Nernst-Planck Continuum Theory for Model Ion Channels
P. Graf, M. G. Kurnikova, R. Coalson, and A. Nitzan,
J. Phys. Chem. B, Vol. 108, pp. 2006-2015 (2004) [PDF]


Accurate theoretical Prediction of Vibrational Frequencies in a Realistic Dynamic Environment: A Case Study of Glutamate in Water Solution and in a Protein-Bound Form
K. Speranskiy, M. Kurnikova
J. Chem. Phys., Vol. 121, pp. 1516-1524 (2004) [PDF]


Role of the Dielectric Barrier in Narrow Biological Channels: A Novel Composite Approach to Modeling Single-Channel Currents.
A. B. Mamonov, R. D. Coalson, A. Nitzan, and M. G. Kurnikova
Biophys. J., Vol. 84, Issue 6, pp. 3646-3661 (2003) [PDF]


Energetics and Dynamics of a Cyclic Oligosaccharide Molecule in a Confined Protein Pore Environment. A Molecular Dynamics Study
I. V. Shilov and M. G. Kurnikova
J. Phys. Chem. B, Vol. 107, Issue 29, pp. 7189-7201 (2003) [PDF]


Three-Dimensional Poisson-Nernst-Planck Theory Studies: Influence of Membrane Electrostatics on Gramicidin A Channel Conductance
A. E. Cardenas, R. D. Coalson, and M. G. Kurnikova
Biophys. J., Vol. 79, pp. 80-93 (2000) [PDF]


A Dynamic Lattice Monte Carlo Model of Ion Transport in Inhomogeneous Dielectric Environments: Method and Implementation
P. Graf, A. Nitzan, M. G. Kurnikova, and R. D. Coalson
J. Phys. Chem. B, Vol. 104, Iss. 51, pp. 12324-12338 (2000) [PDF]


A Lattice Relaxation Algorithm for Three-Dimensional Poisson- Nernst-Planck Theory With Application to Ion Transport Through the Gramicidin A Channel
M. G. Kurnikova, R. D. Coalson, P. Graf, and A. Nitzan
Biophys. J., Vol. 76, Iss. 2, pp. 642-656 (1999) [PDF]


Rotational Relaxation in Polar Solvents. Molecular Dynamics Study of Solute-Solvent Interaction
M. G. Kurnikova, N. Balabai, D. H. Waldeck, and R. D. Coalson
J. Am. Chem. Soc., Vol. 120, Iss. 24, pp. 6121-6130 (1998) [PDF]


Rotational Relaxation of Ionic Molecules in Electrolyte Solutions. Anisotropy Relaxation and Molecular Dynamics Study
N. Balabai, M. G. Kurnikova, R. D. Coalson, and D. H. Waldeck
J. Am. Chem. Soc., Vol. 120, Iss. 31, pp. 7944-7951 (1998) [PDF]


Rotational Diffusion of Organic Solutes: The Role of Dielectric Friction in Polar Solvents and Electrolyte Solutions
N. Balabai, A. Sukharevsky, I. Read, B. Strazisar, M. G. Kurnikova, R. S. Hartman, R. D. Coalson, and D. H. Waldeck
J. Mol. Liquids, Vol. 77, Iss. 1-3, pp. 37-60 (1998) 


Structural Fluctuations, Spin, Reorganization Energy, and Tunneling Energy Control of Intramolecular Electron Transfer: The Surprising Case of Electron Transfer in a D(8)-d(8) Bimetallic System
I. Kurnikov, L. V. Zusman, M. G. Kurnikova, R. S. Farid, and D. Beratan
J. Am. Chem. Soc., Vol. 119, Iss. 24, pp. 5690-5700 (1997) [PDF]


A Molecular Dynamics Study of Photothermal Compression of Colloidal Crystals
J. C. Zahorchak, M. G. Kurnikova, and R. D. Coalson
J. Chem. Phys., Vol. 106, Iss. 4, pp. 1585-1592 (1997) [PDF]


Molecular Dynamics Study of Dielectric Friction
M. G. Kurnikova, D. H. Waldeck, and R. D. Coalson
J. Chem. Phys., Vol. 105, Iss. 2, pp. 628-638 (1996) [PDF]

 

 
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