Understanding motion of intrinsically disordered proteins through simulations.

IDPs (intrinsically disordered proteins) are proteins that lack a rigid structure. In the past two decades, IDPs have been implicated in many diseases ranging from Alzheimer’s to diabetes. In recent years, they have also emerged as potential targets for new therapeutics. There is an urgent need to develop methods to understand the dynamics of disordered proteins. Our research group is primarily engaged in the investigation of protein dynamics and mechanisms through molecular dynamics simulations. We have developed new techniques to analyse the dynamics of proteins using local kinetic networks. The basic ideas have been already tested and implemented on small systems. Our project has two goals. First, the student is expected to test the algorithms on intrinsically disordered protein (IDP) systems. The second part of the project is to build a user-friendly software so that our techniques can be made available to the community of researchers. The project will involve python coding. The student is also expected to learn molecular simulation and analysis techniques.