Molecular dynamics study of intrinsically disordered proteins

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. The extreme structural heterogeneity makes it difficult to use experimental techniques to understand their structure and activity. There is an urgent need to develop methods to understand the dynamics of disordered proteins. Such insights can help us understand the molecular origin of diseases such as diabetes mellitus as well as pave the way for new therapeutics. Our research group is primarily engaged in the investigation of protein dynamics and mechanisms through molecular dynamics simulations. We have developed several new techniques for fine-grained analysis of the dynamics of proteins. The basic ideas have been already tested and implemented on small systems. This M. Tech  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.