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Публикации

2018

  1. P.S. Orekhov, E.G. Kholina, M.E. Bozdaganyan, A.M. Nesterenko, I.B. Kovalenko, and M.G. Strakhovskaya, "Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine Across Bacterial Membranes Revealed by Molecular Dynamics Simulations", J. Phys. Chem. B, accepted manuscript (2018).
  2. A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, J.W. Weisel, and V. Barsegov, "Atomic structural models of fibrin oligomers", Structure, in press (2018).
  3. O. Kononova, F. Maksudov, K.A. Marx and V. Barsegov, "TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid", J. Phys.: Condens. Matter30: 044006 (2018).
  4. M.D. West, I. Labat, H. Sternberg, D. Larocca, I. Nasonkin, K.B. Chapman, R. Singh, E. Makarev, A. Aliper, A. Kazennov, A. Alekseenko, N. Shuvalov, E. Cheskidova, A. Alekseev, A. Artemov, E. Putin, P. Mamoshina, N. Pryanichnikov, J. Larocca, K. Copeland, E. Izumchenko, M. Korzinkin and A. Zhavoronkov, "Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells", Oncotarget9: 7796-7811 (2018).

2017

  1. K.A. Minin, A. Zhmurov, K.A. Marx, P.K. Purohit, and V. Barsegov, "Dynamic transition from α-helices to β-sheets in polypeptide coiled-coil motifs", J. Am. Chem. Soc.139: 16168-16177 (2017).
  2. V. Barsegov, J. Ross, and R. Dima, "Dynamics of microtubules: highlights of recent computational and experimental investigations,", J. Phys.: Condens. Matter29: 433003 (2017).
  3. Y.F. Zuev, R.I. Litvinov, A.E. Sitnitsky, B.Z. Idiyatullin, D.R. Bakirova, D.K. Galanakis, A. Zhmurov, V. Barsegov, and J.W. Weisel, "Conformational Flexibility and Self-Association of Fibrinogen in Concentrated Solutions,", J. Phys. Chem. B121: 7833-7843 (2017).
  4. P. Orekhov, A. Bothe, H.‐J. Steinhoff, K.V. Shaitan, S. Raunser, D. Fotiadis, R. Schlesinger, J.P. Klare, and M. Engelhard, "Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers,", Photochem. Photobiol.93: 796-804 (2017).
  5. O. Kononova, R.I. Litvinov, D.S. Blokhin, V.V. Klochkov, J.W. Weisel, J.S. Bennett, and V. Barsegov, "Mechanistic Basis for the Binding of RGD-and AGDV-Peptides to the Platelet Integrin αIIbβ3", Biochemistry56:1932-1942 (2017).
  6. O. Kononova, K.A. Marx, and V. Barsegov, "Nanoindentation in silico of Biological Particles", in Applied Nanoindentation in Advanced Materials. Editor: Atul Tiwari, John Wiley & Sons (2017).
  7. O. Kononova, A. Zhmurov, K.A. Marx, and V. Barsegov, "Mechanics of Viruses", in Series of Computational Biophysics: Coarse-grained Modeling of Biomolecules. Editors: N. Dokholyan and G. Papoian, Taylor & Francis Publishers (2017).
  8. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov, "An anti-DNA antibody prefers damaged dsDNA over native", J. Biomol. Struct. Dyn.35: 219-232 (2017).

2016

  1. A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, A.R. Mukhitov, J.W. Weisel, and V. Barsegov, "Structural Basis of Interfacial Flexibility in Fibrin Oligomers", Structure24: 1907-1917 (2016).
  2. J. Snijder, O. Kononova, I.M. Barbu, C. Uetrecht, W. F. Rurup, R.J. Burnley, M.S.T. Koay, J.J.L.M. Cornelissen, W.H. Roos, V. Barsegov, G.J.L. Wuite, and A.J.R. Heck, "Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin", Biomacromolecules17: 2522-2529 (2016).
  3. A. Alekseenko, O. Kononova, Y. Kholodov, K.A. Marx, and V. Barsegov, "SOP‐GPU: influence of solvent‐induced hydrodynamic interactions on dynamic structural transitions in protein assemblies", J. Comput. Chem.37: 1537-1551 (2016).
  4. O. Kononova, J. Snijder, Y. Kholodov, K.A. Marx, G.J.L. Wuite, W.H. Roos, and V. Barsegov, "Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles", PLoS Comput. Biol.12: e1004729 (2016).
  5. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov, "Essential Dynamics of DNA-Antibody Complexes", BioNanoScience6: 543-549 (2016).
  6. N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, and R.I. Litvinov, "Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment", Mol. Biol.50: 442-451 (2016).
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