We are interested in predicting the conformational behavior of biological molecules and their interactions. Our main interest is the modelling of G-Protein-Coupled Receptors: from their interactions with extra-cellular ligands to their coupling with intra-cellular partners.
We use All-Atoms MD simulations to sample the conformations of proteins, in their explicit environment (water + membrane atoms included). Classical forces fields are used including that of CHARMM and using different softwares (CHARMM, NAMD, Gromacs).
All-Atoms Molecular Dynamics
Coarse-Grained (CG) MD simulations are useful to reach some time-scales unreachable with AA models. We are using the MARTINI forces field to predict the interactions of GPCRs with their protein partners at the molecular scale and from a dynamical point of view.
Coarse-Grained Molecular Dynamics
NMA is a method of choice to predict the large amplitude (collective motions) of proteins that would not be sampled by classical MD simulations. We developp approaches combining NMA and MD simulations to explore both the local and the global rearrangments of proteins in their explicit environment.
Normal Modes Analysis
Leandro De Oliveira Santos (Post-Doc)
Bartholomé Delort (PhD)
Pedro Renault (Post-Doc)
Landry Charlier (Post-Doc)
Alexandre Perret (M2)
Esra Karakas (M2)
Adriana Garro (Erasmus)