Emblem  Laboratory of Biomolecular Modeling  

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Fusion peptide E5 in the dimyristoylphosphatidylcholine (DMPC) bilayer. Deep insertion of the peptide into the water-lipid interface during MD simulations leads to protruding of some lipid molecules around the binding site into the water phase. This effect is driven by strong electrostatic interactions of negatively charged glutamate residues (especially E11, E15, E19) with cationic chlorine groups of lipids. The water-lipid interface of the monolayer contacting with the peptide is schematically shown with a gray-hatched plane. Water molecules are removed for clarity (Volynsky et al., Biochemistry, 2005).

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