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Our publications

2013

2012

2011

2010

2009

2008

  • Farce A., Chugunov A.O., Logé C., Yous S., Vergoten G., Efremov R.G., Lesieur D., Chavatte P. Homology Modeling of MT1 and MT2 Receptors (2008). Eur. J. Med. Chem. 43, 1926–1944 (See @ medline).
  • Pyrkov T.V., Priestle J., Jacoby E., Efremov R.G. Ligand-specific scoring functions: Improved ranking of docking solutions. (2008). SAR and QSAR in Environmental Research. 19, 91–99 (See @ medline).
  • Bocharov E.V., Mineev K.S., Volynsky P.E., Ermolyuk Ya.S., Tkach E.N., Sobol A.G., Chupin V.V., Kirpichnikov M.P., Efremov R.G., Arseniev A.S. Spatial structure of dimeric transmembrane domain of growth factor receptor ErbB2. (2008). J. Biol. Chem. 283, 6950–6956 (See @ medline).
  • Dubovskii P.V., Volynsky P.E., Polyansky A.A., Karpunin D.V., Chupin V.V., Efremov R.G., Arseniev A.S. 3D Structure/Hydrophobicity of Latarcins Specifies their Mode of Membrane Activity. (2008). Biochemistry 47, 3525–3533 (See @ medline).
  • Bocharov E.V., Mayzel M.L., Volynsky P.E., Goncharuk M.V., Ermolyuk Ya.S., Schulga A.A., Artemenko E.O., Efremov R.G., Arseniev A.S. Spatial Structure and pH-Dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1. (2008). J. Biol. Chem. 283, 29385–29395 (See @ medline).

2007

  • Efremov R.G., Volynsky P.E., Polyansky A.A., Nolde D.E., Arseniev A.S. Protein-membrane interactions: lessons from in silico studies. In: “Structure and Biophysics—New Technologies for current Challenges in Biology and Beyond”. Puglisi J.D. (Ed.), Springer 2007. pp. 19–39 (doi: 10.1007/978-1-4020-5900-1_3).
  • Bocharov E.V., Pustovalova Yu.E., Pavlov K.V., Volynsky P.E., Goncharuk M.V., Ermolyuk Ya.S., Karpunin D.V., Shulga A.A., Kirpichnikov M.P., Efremov R.G., Maslennikov I.V., Arseniev A.S. (2007). Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger. J. Biol. Chem. 282, 16256–16266 (See @ medline);
  • Vereshaga Ya.A., Volynsky P.E., Pustovalova Ju.E., Nolde D.E., Arseniev A.S., Efremov R.G. (2007). Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins: Structure, Function, and Bioinformatics 69, 309–325 (See @ medline).
  • Efremov R.G., Volynsky P.E., Nolde D.E., Vergoten G., Arseniev A.S. (2007). The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding. J. Biomol. Struct. & Dynamics 25, 195–206 (See @ medline).
  • Chugunov, A.O., Novoseletsky, V.N., Nolde, D.E., Arseniev, A.S., Efremov, R.G. (2007). A method to assess packing quality of transmembrane α-helices in proteins. I. Parameterization using structural data. J. Chem. Inf. Model. 47, 1150–1162 (doi: 10.1021/ci600516x).
  • Chugunov, A.O., Novoseletsky, V.N., Nolde, D.E., Arseniev, A.S., Efremov, R.G. (2007). A method to assess packing quality of transmembrane α-helices in proteins. II. Validation by “correct vs. misleading” test. J. Chem. Inf. Model., 47, 1163–1170 (doi: 10.1021/ci600517c).
  • Pyrkov, T.V., Kosinsky, Yu.A, Arseniev, A.S., Priestle, J.P., Jacoby, E., Efremov, R.G. (2007). Docking of ATP to Ca-ATPase: Considering Protein Domain Motions. J. Chem. Inf. Model., 47, 1171–1181 (doi: 10.1021/ci700067f).
  • Pyrkov T.V., Efremov R.G. Fragment-Based Scoring Function to Re-rank Results of Docking ATP. (2007). Int. J. Mol. Sci. v. 8, 1083–1094 (doi: 10.3390/i8111083).
  • Efremov R.G., Chugunov A.O., Pyrkov T.V., Priestle J.P., Arseniev A.S., Jacoby E. Molecular lipophilicity in protein modeling and drug design. (2007). Curr. Med. Chem. 14(4), 393–415 (See @ medline).
  • Chugunov, A.O., Novoseletsky, V.N., Arseniev, A.S., Efremov, R.G. (2007). A Novel Method for Packing Quality Assessment of Transmembrane α-Helical Domains in Proteins. Biochemistry (Moscow) V. 72(3), 293–300 (DOI: 10.1134/S0006297907030066).
  • Polyansky A.A., Volynsky P.E., Efremov R.G. Computer simulations of membrane-lytic peptides: perspectives in drug design. (2007). J. Bioinform. & Comput. Biology 5, 611–626 (See @ medline).
  • Pyrkov T.V., Kosinsky Yu.A., Arseniev A.S., Priestle J.P., Jacoby E., Efremov R.G. Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. (2007) Proteins: Structure, Function, and Bioinformatics 66(2), 388–398. See @ medline.

2005—2006

  • Chugunov A.O., Chavatte P., Farce A., Efremov R.G. Differences in binding sites of two melatonin receptors help to explain their selectivity to some melatonin analogs: a molecular modeling study. (2006) J. Biomol. Struct. & Dynamics 24, 91-108. See @ medline.
  • Dubovskii P.V., Volynsky P.E., Polyansky A.A., Chupin V.V., Efremov R.G., Arseniev A.S. Spatial structure and activity mechanism of a novel spider antimicrobial peptide. (2006). Biochemistry 45, 10759-10767. See @ medline.
  • Volynsky P.E., Bocharov E.V., Nolde D.E., Vereshaga Ya.A., Mayzel M.L., Mineev K.S., Mineeva E.A., Pustovalova Yu.E., Gagnidze I.A., Efremov R.G., Arseniev A.S. Solution of the spatial structure of dimeric transmembrane domains of proteins by heteronuclear NMR spectroscopy and molecular modeling. (2006) Biophysics (Russian). V. 51 Suppl. 1, S23–S27 (doi: 10.1134/S0006350906070050).
  • Efremov R.G., Vereshaga Y.A., Volynsky P.E., Nolde D.E., Arseniev A.S. Association of transmembrane helices: what determines assembling of a dimer? (2006) J. Comput. Aid. Mol. Design 20, 27-45. See @ medline.
  • Dubovskii P.V., Lesovoy D.M., Dubinnyi M.A., Konshina A.G., Utkin Y.N., Efremov R.G., Arseniev A.S. Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins. (2005). Biochem. J. 387, Part 3, p. 807-815. See @ medline.
  • Polyansky A.A., Volynsky P.E., Nolde D.E., Arseniev A.S., Efremov R.G. The Role of Lipid Charge in Organization of Water/Lipid Bilayer Interface: Insights via Computer Simulations. (2005). J. Phys. Chem. B, 109(31), p. 15052-15059. DOI:10.1021/jp0510185.
  • Vereshaga, Y.A., Volynsky P.E., Nolde D.E., Arseniev A.S., Efremov R.G. Helix interactions in membranes: lessons from unrestrained Monte Carlo simulations. (2005). J. Chem. Theory & Comput. 1(6), p. 1252-1264. DOI:10.1021/ct0501250.
  • Volynsky P.E., Polyansky A.A., Simakov N.A., Arseniev A.S., Efremov R.G. Effect of lipid composition on the «membrane response» induced by a fusion peptide. (2005). Biochemistry 44(44), p. 14626–14637. See @ medline
  • Chugunov A., Chavatte P., Efremov R. Molecular modeling of human MT1 and MT2 melatonin receptors. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, p. 259-270. DOI: 10.1007/0-387-29455-4_26
  • Polyansky A.A., Volynsky P.E., Arseniev A.S., Efremov R.G. Computer simulations of anionic unsaturated lipid bilayer — a suitable model to study membrane interactions with a cell-penetrating peptide. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, p. 235-246. DOI: 10.1007/0-387-29455-4_24

2003—2004

  • Tsivkovskii R., Efremov R.G., Lutsenko S. The Role of Invariant His1069 in Folding and Function of the Wilson’s disease Protein, the Human Copper-transporting ATPase ATP7B. J. Biol. Chem. (2003). 278, 13302-8.
  • Konshina A.G., Volynsky P.E., Arseniev A.S., Efremov R.G. Interaction of Cardiotoxin A5 with Membrane: Role of Conformational Heterogeneity and Hydrophobic Properties. (2003). Russian J. Bioorg. Chem. 29(6), 523-533. DOI:10.1023/B:RUBI.0000008892.75272.ab.
  • Dioubankova N.N., Malakhov A.D., Stetsenko D.A., Gait M.J., Volynsky P.E., Efremov R.G., Korshun V.A. Pyrenemethyl ara-Uridine-2’-carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex. (2003) ChemBioChem 4:841-847. See @ medline.
  • Polyansky A.A., Kosinsky Yu.A., Efremov R.G. Correlation of Local Changes in the Temperature-Dependent Conformational Flexibility of Thioredoxins with Their Thermostability. (2004). Russian J. Bioorg. Chem. 30(5), 421-430. DOI:10.1023/B:RUBI.0000043784.51859.41.
  • Efremov R.G., Nolde D.E., Konshina A.G., Syrtcev N.P., Arseniev A.S. Peptides and proteins in membranes: what can we learn via computer simulations? (2004) Curr. Med. Chem., 11(18), 2421-2442. See @ medline.
  • Kosinsky Yu.A., Volynsky P.E., Lagant P., Vergoten G., Suzuki E., Arseniev A.S., Efremov R.G. Development of the Force Field Parameters for Phosphoimidazole and Phosphohistidine. (2004) J. Comput. Chem., 25(11), 1313-1321. See @ medline.
  • Efremov, R. G., Kosinsky Yu.A., Nolde D.E., Tsivkovskii, R., Arseniev A.S., Lutsenko, S. Molecular Modeling of the Nucleotide-Binding Domain of the Wilson’s Disease Protein: Location of the ATP-binding Site, Domain Dynamics, and Potential Effects of the Major Disease Mutations. (2004) Biochem. J. 382, Part I, 293-305. DOI:10.1042/BJ20040326.
  • Morgan C.T., Tsivkovskii R., Kosinsky Yu.A., Efremov R.G., Lutsenko S. The Distinct Functional Properties of the Nucleotide-binding Domain of ATP7B, the Human Copper-transporting ATPase. Analysis of the Wilson disease mutations E1064A, H1069Q, R1151H, and C1104F. (2004) J. Biol. Chem. 279(35), 36363-36371. See @ medline.
  • Efremov R.G., Nolde D.E., Volynsky P.E., Vereshaga Y.A., Simakov N.A., Polyansky A.A. Molecular modeling of membrane peptides and proteins. (2004). Fundametal and Clinical Pharmacology, 18, p. 594. DOI:10.1111/j.1472-8206.2004.00288.x.

2000—2002

  • Efremov R.G., Nolde D.E., Volynsky P.E., Arseniev A.S. Modeling of peptides in implicit membrane-mimetic media. Molecular Simulation (2000). 24, 275-291.
  • Kosinsky Yu.A., Dubovskii P.V., Nolde D.E., Arseniev A.S., Efremov R.G. Fusion peptide interaction with lipid bilayer: modeling with Monte Carlo simulation and continuum electrostatics calculation. Molecular Simulation (2000). 24, 341-349.
  • Nolde, D.E., P.E. Volynsky, A.S. Arseniev, and R.G. Efremov. Modeling of peptides and proteins in a membrane environment: I. A solvation model mimicking a lipid bilayer. Russian J. Bioorg. Chem. (2000) 26, 115-124. See @ medline.
  • Volynskii P.E., Nolde D.E., Arseniev A.S., Efremov R.G. Modeling of peptides and proteins in a membrane environment. II. Structural and energetic aspects of Glycophorin A in a lipid bilayer. Russian J. Bioorg. Chem. (2000) 26, 163-172. See @ medline.
  • Efremov R.G., Volynsky P.E., Nolde D.E., Arseniev A.S. Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimic media. Theor. Chem. Acc. (2001a). 106, 48-54. See @ Springer Link.
  • Efremov R.G., Volynsky P.E., Dauchez M.A.M., Nolde D.E., Arseniev A.S., Alix A.J.P. Assessment of conformation and energetics of the N-terminal part of elafin via computer simulations. Theor. Chem. Acc. (2001b). 106, 55-61. See @ Springer Link.
  • Efremov R.G., Volynsky P.E., Nolde D.E., Dubovskii P.V., Arseniev A.S. Interaction of cardiotoxins with membranes: a molecular modeling study. Biophys. J. (2002a). 83, 144-153. See @ medline.
  • Efremov R.G., Volynsky P.E., Nolde D.E., van Dalen A., de Kruijff B., Arseniev A.S. Monte Carlo simulations of voltage-driven translocation of a signal sequence. FEBS Lett. (2002b). 526, 97-100. See @ medline.
  • Shenkarev Z.O., Balashova T.A., Efremov R.G., Yakimenko Z.A., Ovchinnikova T.V., Raap J., Arseniev A.S. Spatial structure of Zervamicin IIB bound to DPC micelles. Implications for voltage-gating. Biophys. J. (2002). 82, 762-771. See @ medline.
  • Abdullaev Z.Kh., Bodrova M.E., Chernyak B.V., Dolgikh D.A., Kluck R.M., Pereverzev M.O., Arseniev A.S., Efremov R.G., Kirpichnikov M.P., Mokhova E.N., Newmeyer D.D., Roder H., Skulachev V.P. A cytochrome c mutant of high electron transfer and antioxidant activities which is completely devoid apoptogenic effect. Biochem. J. (2002). 362, 749-754. See @ medline.
  • Lutsenko S., Efremov R.G., Tsivkovskii R., Walker J.M. Human copper-transporting ATPase ATP7B (the Wilson’s disease protein): Biochemical properties and regulation. J. Bioenerg. Biomemb. (2002). 34 (5), 351-362. .

1990-s

  • Efremov R.G., Gulyaev D.I., Vergoten G., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. I. Hydrophobic properties of transmembrane segments of Na,K-ATPase. J. Protein Chemistry. (1992a). 11, 665-675. See @ medline.
  • Efremov R.G., Gulyaev D.I., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na,K-ATPase. J. Protein Chemistry. (1992b). 11, 699-708.
  • Modyanov N.N., Vladimirova N.M., Gulyaev D.I., Efremov R.G. Architecture of the Sodium Pump: vectorial labeling and computer modeling. Ann. New York Acad. Sci. (1992). 671, 134-146.
  • Efremov R.G., Alix A.J.P. Environmental characteristics of residues in proteins. J. Biomol. Struct. & Dynamics. (1993), 11, 483-507. See @ medline.
  • Efremov R.G., Gulyaev D.I., Modyanov N.N. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. III. Modeling of intramembrane moiety of Na,K-ATPase. J. Protein Chemistry. (1993). 12, 143-152.
  • Efremov R.G., Vergoten G. The hydrophobic nature of membrane-spanning a-helices as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis. J. Physical Chemistry. (1995). 99, 10658-10666.
  • Golovanov A.P., Efremov R.G., Jaravine V.A., Vergoten G., Arseniev A.S. Amino acid residue: is it structural or functional? FEBS Lett. (1995), 375, 162-166. See @ medline.
  • Efremov R.G., Golovanov A.P., Vergoten G., Alix A.J.P., Tsetlin V.I., Arseniev A.S. Detailed assessment of spatial hydrophobic and electrostatic properties of 2D NMR-derived models of neurotoxin II. J. Biomol. Struct. & Dynamics. (1995), 12, 971-991.
  • Efremov R.G., Vergoten G. Hydrophobic organization of membrane helix bundle in bacteriorhodopsin. J. Protein Chemistry. (1996a). 15, 1, 63-76. See @ medline.
  • Efremov R.G., Vergoten G. Recognition of transmembrane a-helical segments with environmental profiles. Protein Engineering. (1996b). 9, 253-263. See @ Protein Engineering.
  • Nolde D.E., Arseniev A.S., Vergoten G., Efremov R.G. Atomic solvation parameters for protein in a membrane environment. Application to transmembrane a-helices. J. Biomol. Struct. & Dynamics. (1997). 15, p. 1-18. See @ medline.
  • Golovanov A.P., Efremov R.G., Jaravine V.A., Vergoten G., Kirpichnikov M.P., Arseniev A.S. A new method to characterize hydrophobic organization of proteins: Application to rational protein engineering of barnase. J. Biomol. Struct. & Dynamics. (1998). 15, 673-687. See @ medline.
  • Efremov R.G., Legret F., Vergoten G., Capron A., Bahr G.M., Arseniev A.S. Molecular modeling of HIV-1 coreceptor CCR5 and exploring of conformational space of its extracellular domain in molecular dynamics simulation. J. Biomol. Struct. & Dynamics. (1998). 16, 77-90.
  • Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. Peptides in membranes: assessment of the effects of environment via simulations with implicit solvation model. Theor. Chem. Acc. (1999a). 101, 170-174. See @ Springer Link.
  • Efremov R.G., Vergoten G., Arseniev A.S. A new "hydrophobic template" method detects segments forming transmembrane alpha-helical bundles in ion channels. Theor. Chem. Acc. (1999b). 101, 73-76. See @ Springer Link.
  • Efremov, R.G., Nolde, D.E., Vergoten G., Arseniev, A.S. A solvent model for simulations of peptides in bilayers. I. Testing on model systems. Biophys. J. (1999c). 76, 2448-2459. See @ Biophysical Journal.
  • Efremov, R.G., Nolde, D.E., Vergoten G., Arseniev, A.S. A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices. Biophys. J. (1999d). 76, 2460-2471. See @ Biophysical Journal.
  • Efremov R.G., Truong M.-J., Darcissac E.C.A., Zeng J., Grau O., Vergoten G., Debard C., Capron A., Bahr G.M. Human chemokine receptors CCR5, CCR3, and CCR2B share common polarity motif in the first extracellular loop with other human GPCRs: implications for HIV-1 coreceptor function. Eur. J. Biochem. (1999e). 263, 746-756. See @ EJB.
  • Efremov R.G., Nolde D.E., Volynsky P.E., Chernyavsky A.A., Dubovsky P.V., Arseniev A.S. Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin. FEBS Lett. (1999f). 462, 205-210. See @ Elsevier.
  • Golovanov A.P., Volynsky P.E., Ermakova S.B., Arseniev A.S. (1999). Protein Eng. 12, 31-40. See @ medline.

Address: 117997 Russia, Moscow, ul. Miklukho-Maklaya 16/10.
Tel.: +7 (495) 336-20-00.
Email: efremov@nmr.ru

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