Emblem  Laboratory of Biomolecular Modeling  

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Binding of antimicrobial peptides (latarcins, Ltcs) to the sodiumdodecyl sulfate micelle (SDS, 60 detergent molecules) as revealed by molecular dynamics (MD) simulations. Final MD-structures of Ltcs are the result of their fine-tuned interactions with the heterogeneous water-detergent interface. Thus, rigid amphipatic helix of Ltc1 retains rod-like conformation in the micelle, whereas flexible Ltc2a forms kinked conformation adapting to polar/hydrophobic properties of the micelle surface. Cationic, hydrophobic and polar residues are shown in stick representation. Solvent accessible surface of SDS micelle is colored as follows: polar heads — red, acyl chains — gray (Polyansky et al., JBCB, 2007).

Our main interests include computer simulations of membrane and membrane-active peptides and proteins, especially development of protein solvation models for membrane-mimic media. Among the objects we are working on: cardiotoxins, fusion peptides, seven-helix receptors of the GPCR family, glycophorin A and its dimers, signal peptides.

Among our objectives is understanding of spatial structure-function relationships for membrane proteins via molecular modeling techniques.

Research activities:

  • Membrane peptides and proteins: structure, mode of membrane binding, simulation of functioning;
  • Hydrophobic/hydrophilic organization of globular and membrane proteins;
  • Homology modeling of proteins;
  • Computer-aided bioengineering of proteins: design of functionally important mutations and chimeric proteins.


  • Monte Carlo and molecular dynamics in implicit and explicit solvents (including biomembranes);
  • Sequence-based protein structure prediction and threading;
  • Molecular docking and activity prediction;
  • Assessment of protein electrostatics and thermostability;
  • Quantum chemical calculations;
  • Molecular hydrophobicity potential calculations.

For more information see our projects.

See our computational facilities and software.

Find out how to contact us.

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

© 2003–2007