Нольде Дмитрий Евгеньевич

Образование

Период обученияСтрана, городУчебное заведениеДополнительная информация
1986–1992 Россия, г. Долгопрудный Московской обл. Московский физико-технический институт

Избранные публикации

  1. Панина ИС, Нольде ДЕ, Чугунов АО, Ефремов РГ (2016). Структурно-динамическая модель комплекса лантибиотика низин с липидом-II в биомембране. 1 (0), 263–267
  2. Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG (2016). Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 6 (0), 33112
  3. Polyansky AA, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG (2014). PREDDIMER: A web server for prediction of transmembrane helical dimers. Bioinformatics 30 (6), 889–890
  4. Chugunov A, Pyrkova D, Nolde D, Polyansky A, Pentkovsky V, Efremov R (2013). Lipid-II forms potential "landing terrain" for lantibiotics in simulated bacterial membrane. Sci Rep 3 (0), 1678
  5. Чугунов АО, Нольде ДЕ, Пыркова ДВ, Полянский АА, Пентковский ВМ, Ефремов РГ (2013). На пути к новым антибиотикам. 12 (0), 34–36
  6. Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Pentkovsky VM, Efremov RG (2013). Dynamic clustering of lipids in hydrated two-component membranes: Results of computer modeling and putative biological impact. J Biomol Struct Dyn 31 (1), 87–95
  7. Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Efremov RG (2013). Lateral heterogeneity as an intrinsic property of hydrated lipid bilayers: A molecular dynamics study.  (0), 85–101
  8. Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Efremov RG (2012). Lateral heterogeneity as an intrinsic property of hydrated lipid bilayers: A molecular dynamics study.  (0), 85–101
  9. Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Efremov RG (2011). Lateral clustering of lipids in hydrated bilayers composed of dioleoylphosphatidylcholine and dipalmitoylphosphatidylcholine. BIOL MEMBRANY 28 (4), 298–306
  10. Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Efremov RG (2011). Lateral clustering of lipids in hydrated bilayers composed of dioleoylphosphatidylcholine and dipalmitoylphosphatidylcholine. Biochem (Mosc) Suppl Ser A Membr Cell Biol 5 (3), 278–285
  11. Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG (2009). Complementarity of hydrophobic/hydrophilic properties in protein-ligand complexes: A new tool to improve docking results. Vierteljahrschr Soz Wirtschaftsgesch  (0), 21–41
  12. Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG (2009). PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 25 (9), 1201–1202
  13. Vereshaga YA, Volynsky PE, Pustovalova JE, Nolde DE, Arseniev AS, Efremov RG (2007). Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: A molecular modeling study. Proteins 69 (2), 309–325
  14. Chugunov AO, Novoseletsky VN, Nolde DE, Arseniev AS, Efremov RG (2007). Method to assess packing quality of transmembrane α-helices in proteins. 2. Validation by "correct vs misleading" test. J Chem Inf Model 47 (3), 1163–1170
  15. Chugunov AO, Novoseletsky VN, Nolde DE, Arseniev AS, Efremov RG (2007). Method to assess packing quality of transmembrane a-helices in proteins. 1. Parametrization using structural data. J Chem Inf Model 47 (3), 1150–1162
  16. Efremov RG, Volynsky PE, Nolde DE, Vergoten G, Arseniev AS (2007). The membrane-proximal fusion domain of hiv-1 gp41 reveals sequence-specific and fine-tuning mechanism of membrane binding. J Biomol Struct Dyn 25 (2), 195–205
  17. Volynsky PE, Bocharov EV, Nolde DE, Vereschaga YA, Mayzel ML, Mineev KS, Mineeva EA, Pustovalova YE, Gagnidze IA, Efremov RG, Arseniev AS (2006). Solution of the spatial structure of dimeric transmembrane domains of proteins by heteronuclear NMR spectroscopy and molecular modeling. Biophysics (Oxf) 51 (1), 23–27
  18. Efremov RG, Vereshaga YA, Volynsky PE, Nolde DE, Arseniev AS (2006). Association of transmembrane helices: What determines assembling of a dimer? J Comput Aided Mol Des 20 (1), 27–45
  19. Vereshaga YA, Volynsky PE, Nolde DE, Arseniev AS, Efremov RG (2005). Helix interactions in membranes: Lessons from unrestrained Monte Carlo simulations. J Chem Theory Comput 1 (6), 1252–1264
  20. Polyansky AA, Volynsky PE, Nolde DE, Arseniev AS, Efremov RG (2005). Role of lipid charge in organization of water/lipid bilayer interface: Insights via computer simulations. J Phys Chem B 109 (31), 15052–15059
  21. Efremov RG, Kosinsky YA, Nolde DE, Tsivkovskii R, Arseniev AS, Lutsenko S (2004). Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: Location of the ATP-binding site, domain dynamics and potential effects of the major disease mutations. Biochem J 382 (1), 293–305
  22. Lagant P, Nolde D, Stote R, Vergoten G, Karplus M (2004). Increasing normal modes analysis accuracy: The SPASIBA spectroscopic force field introduced into the CHARMM program. J Phys Chem A 108 (18), 4019–4029
  23. Efremov RG, Nolde DE, Konshina AG, Syrtcev NP, Arseniev AS (2004). Peptides and proteins in membranes: What can we learn via computer simulations? Curr Med Chem 11 (18), 2421–2442
  24. Efremov RG, Volynsky PE, Nolde DE, Van Dalen A, De Kruijff B, Arseniev AS (2002). Monte Carlo simulations of voltage-driven translocation of a signal sequence. FEBS Lett 526 (13), 97–100
  25. Efremov RG, Volynsky PE, Nolde DE, Dubovskii PV, Arseniev AS (2002). Interaction of cardiotoxins with membranes: A molecular modeling study. Biophys J 83 (1), 144–153
  26. Efremov RG, Volynsky PE, Dauchez MAM, Nolde DE, Arseniev AS, Alix AJP (2001). Assessment of conformation and energetics of the N-terminal part of elafin via computer simulations. Theor Chem Acc 106 (12), 55–61
  27. Efremov R, Volynsky P, Nolde D, Vergoten G, Arseniev A (2001). Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimetic media. Theor Chem Acc 106 (12), 48–54
  28. Nolde DE, Volynskii PE, Arseniev AS, Efremov RG (2000). Modeling of peptides and proteins in membrane environment. I. A solvation model mimicking a lipid bilayer. Bioorg Khim 26 (2), 140
  29. Volynskii PE, Nolde DE, Arseniev AS, Efremov RG (2000). Modeling of peptides and proteins in a membrane environment. II. Structural and energetic aspects of glycophorin A in a lipid bilayer. Bioorg Khim 26 (3), 171–172
  30. Volynskii PE, Nolde DE, Arseniev AS, Efremov RG (2000). Modeling of peptides and proteins in a membrane environment: II. Structural and energetic aspects of glycophorin A in a lipid bilayer. Russ. J. Bioorganic Chem. 26 (3), 143–151
  31. Nolde DE (2000). Modeling of peptides and proteins in a membrane environment: I. A solvation model mimicking a lipid bilayer. Russ. J. Bioorganic Chem. 26 (2), 115–124
  32. Efremov RG, Nolde DE, Volynsky PE, Chernyavsky AA, Dubovskii PV, Arseniev AS (1999). Factors important for fusogenic activity of peptides: Molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin. FEBS Lett 462 (12), 205–210
  33. Efremov RG, Nolde DE, Vergoten G, Arseniev AS (1999). A solvent model for simulations of peptides in bilayers. I. Membrane- promoting α-helix formation. Biophys J 76 (5), 2448–2459
  34. Efremov RG, Nolde DE, Vergoten G, Arseniev AS (1999). A solvent model for simulations of peptides in bilayers. II. Membrane- spanning α-helices. Biophys J 76 (5), 2460–2471
  35. Efremov RG, Nolde DE, Vergoten G, Arseniev AS (1999). Peptides in membranes: Assessment of environmental effects via simulations using an implicit solvation model. Theor Chem Acc 101 (13), 170–174
  36. Reibarkh MY, Nolde DE, Vasilieva LI, Bocharov EV, Shulga AA, Kirpichnikov MP, Arseniev AS (1998). Three-dimensional structure of binase in solution. FEBS Lett 431 (2), 250–254
  37. Reibarkh MY, Nolde DE, Bocharov EV, Vasileva LI, Shulga AA, Kirpichnikov MP, Arseniev AS (1997). The Secondary Structure of Binase in Solution Determined by1H NMR. Bioorg Khim 23 (10), 794
  38. Reibarkh MY, Nolde DE, Bocharov EV, Vasileva LI, Shulga AA, Kirpichnikov MP, Arseniev AS (1997). The secondary structure of binase in solution determined by1H NMR. Russ. J. Bioorganic Chem. 23 (10), 706–717
  39. Jaravine VA, Nolde DE, Reibarkh MJ, Korolkova YV, Kozlov SA, Pluzhnikov KA, Grishin EV, Arseniev AS (1997). Three-dimensional structure of toxin OSK1 from Orthochirus scrobiculosus scorpion venom. Biochemistry 36 (6), 1223–1232
  40. Orekhov VY, Nolde DE, Golovanov AP, Korzhnev DM, Arseniev AS (1995). Processing of heteronuclear NMR relaxation data with the new software DASHA. Appl Magn Reson 9 (4), 581–588
  41. Nolde DE, Sobol AG, Pluzhnikov KA, Grishin EV, Arseniev AS (1995). Three-dimensional structure of ectatomin from Ectatomma tuberculatum ant venom. J Biomol NMR 5 (1), 1–13
  42. Arseniev AS, Pluzhnikov KA, Nolde DE, Sobol AG, Torgov MY, Sukhanov SV, Grishin EV (1994). Toxic principle of selva ant venom is a pore-forming protein transformer. FEBS Lett 347 (23), 112–116
  43. BARSUKOV IL, NOLDE DE, LOMIZE AL, ARSENIEV AS (1992). Three‐dimensional structure of proteolytic fragment 163–231 of bacterioopsin determined from nuclear magnetic resonance data in solution. FEBS J 206 (3), 665–672