We study the structure, dynamics, and interactions of biological macromolecules using a range of molecular modeling tools, including structural bioinformatics and molecular simulations. We also develop our own tools, both in the area of bioinformatics and in molecular simulations. Our ultimate goal is to better understand of the links between structure, interactions and, ultimately, biological functions at the molecular level. Our main activities focus on:
Biomembranes: structure, dynamics, and interactions
Biological membranes envelop and compartmentalize all living cells. Biomembranes are extremely dynamic entities at all levels – in fact the vast majority of them is liquid, in physiologically relevant states, which makes it very challenging to obtain structural information at high resolution with experimental techniques. We use molecular simulations at multiple levels, from quantum mechanics to all-atom and coarse-grained molecular dynamics simulations, to gain insight into membrane structure, dynamics, interactions, and transformations.
The main focus is on the prediction of protein-protein interactions (PPI), at the molecular level (assessment of docking methods) and at the cellular level (development of bioinformatics methods to predict PPI networks). The latter uses sequence similarity between a set of interacting proteins (reference PPI) and the proteins of the organism under scrutiny to infer interaction between its proteins.