Many proteins, such as enzymes, receptors, transporters, antigens etc., interact with a very large scale of specific ligands through unique domains that function as specialized binding sites. These binding interactions necessitate a coordinated flexing of the substrate molecule together with conformational fluctuations of the protein. Since the initial steps leading to recognition between the two interacting molecules are too fast to be experimentally recorded, we use various computational techniques, mainly, MD simulations, NMA and docking algorithms, to follow the conformation landscape of protein structures. Based on our calculations, we quantitate the physical properties of the system investigated, revealing the biochemical mechanism at atomic scale resolution.
Currently, we are studying several subjects, for example: Integrin activation; the recognition and interaction of SARS-Corona Virus and its antibody; conformational changes in gp120 envelope protein of HIV virus; and the mechanism of drug resistance of MRP1;