Emblem  Laboratory of Biomolecular Modeling  

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Results of Monte Carlo simulations of cytotoxin II from asian cobra Naja oxiana in membrane-mimic media. Starting (left), intermediate (middle), and lowest-energy (right) states. Nonpolar layer of membrane is gray hatched.

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