Research

Structural Bioinformatics

Structural and theoretical analyses of proteins are central to the understanding of complex molecular mechanisms and are fundamental to the drug discovery process. Computational techniques yield useful insights into an ever-wider range of biomolecular systems. Protein three-dimensional structures and molecular functions can be predicted in some circumstances, while experimental structures can be analyzed in depth via such computational approaches. Non-covalent binding of biomolecules can be understood by considering structural, thermodynamic and kinetic issues, and theoretical simulations of such events can be attempted. The central role of electrostatic interactions with regard to protein function, structure and stability has been investigated and some electrostatic properties can be modeled theoretically. Computer methods thus help to prioritize, design, analyze and rationalize biochemical experiments. We use and develop molecular modeling methods to analyze protein structures, homology modeling, molecular dynamics, Monte Carlo simulations, electrostatics, protein docking.

For instance, we have been using protein docking to investigate the tenase and prothrombinase complexes. You can see Autin L et a., Proteins, 2006, 63:440-50 (PDF here) and Autin L et al., J Thromb Haemost. 2005, 3:2044-56 (here). For MD simulations, investigation of point mutations and electrostatic computations, you can see Miteva M. et al., Nucleic Acids Res. 2005, 33: W372-5 (here) and Miteva M. et al.,  Biophys J. 2004, 86:488-98 (here)