home / work / projects (↓ see list)

Our projects

Monte Carlo simulations of proteins in implicit membrane-mimic media

• Implicit membrane model;
• Binding of α-helical peptides and proteins to membranes;
• Interactions of β-sheet cardiotoxins with implicit membrane;
• Protein-protein interactions in implicit bilayer: homodimer of human glycophorin A;
• Role of transmembrane voltage in signal peptide insertion;

Molecular dynamics (MD) simulations of explicit membrane systems

• Application of MD simulations technique in studies of protein–membrane interactions. Validation of results;
• Full-atom models of membranes (lipid bilayers, micelles and cell membrane mimics);
• Membrane-active proteins and peptides (MAP) in model membranes;
• Protein–protein interactions in membrane enviroment.

Assessment of detailed hydrophobic/hydrophilic properties of globular and membrane proteins

• Molecular hydrophobicity potential approach;
• Analysis of hydrophobic organization of proteins;
• The “hydrophobicity template” method;
• Recognition of transmembrane α-helices with environmental profiles.

Ligand—protein interactions

• Molecular simulation of ATP—ATPase interaction;
• Hydrophobic complementarity in ATP—protein complexes.

Electrostatic interactions in neurotoxin II from asian cobra Naja oxiana

Molecular modeling of membrane proteins

• Molecular modeling of melatonin receptors;
• Algorithm to assess packing quality of α-helical transmembrane domains.

In silico prediction of single-point mutations enchancing protein thermostability

© 2003–2007
batch2k.