Molecular: Computational studies of membrane protein-ligand interactions

The goal of our research is to improve atomic-level understanding of receptor-ligand interactions using computational models. Using methods such as molecular dynamics simulations, molecular docking, and homology modeling we model how small molecules interact with proteins and thereby modulate their function. In particular, we focus on membrane proteins such as G protein-coupled receptors (GPCRs) and ligand-gated ion channels, which are important targets for drug development.

Recent projects (2012-2013):

(I) We are interested in the role of conserved residues and water in the GPCRs activation mechanism. To study the activation process, we use molecular dynamics simulations in combination with free energy calculations. Our simulations have provided new insights into GPCR function.

(2) We are using molecular dynamics simulations to improve the description of water and receptor flexibility in molecular docking algorithms. Our results show that molecular dynamics simulations can give detailed information about water molecules in binding sites. A new energy term based on simulations will be included in our predictions of protein-ligand binding affinities to improve the performance of molecular docking in drug discovery.