COMPDESIGN · Statistical physics-based computational design of protein-RNA complexes

This project aims to computationally design RNA molecules apt to bind to a given protein under given conditions (such as binding affinity, properties of the solution and temperature).The relevance of this research lies in the current effort to elucidate the mechanism that guide RNA-protein complexes, which are abundantly found in the cell at all levels of relevant cell mechanisms. Further, such a study is expected to be a first valuable step in the effort of rational drug design in silico.In this project, we propose to transfer concepts from statistical mechanics used in e.g. soft matter science, to this challenging problem. Such a physics-based approach will explicitly take into account entropic effects encountered in the RNA-protein complexes, which properly account for the flexibility of these biomolecules, but which are usually disregarded by current techniques. With such an approach, we aim to win physical insight into the mechanisms governing RNA-protein complexes (shown on the example of the Hfq-RNA complex). Then, simulations can help to overcome experimental bottlenecks and drive their progress.In this project, the applicant aims to maintain close contacts with both other theoreticians and with the relevant experimental groups, both at the host institution and within the European Community.