Coarse-grained modelling of protein dynamics and interactions

We develop coarse-grained models with different levels of resolution and enhanced sampling algorithms to study efficiently large scale protein conformational transitions, protein aggregation, macromolecular assemblies and protein-protein interactions in very large systems.

Large systems and long timescales that would demand an unfeasible simulation time with usual atomistic molecular dynamics methods become feasible when using coarse-grained representations of the system with a lower resolution than the atomistic representation used in standard molecular dynamics simulations.

We use several types of coarse-grained representations of the structures for generating realistic large-scale conformational transition pathways [1], [2], multiscale representations with different levels of coarse-graining in the system to account for flexibilty in protein-protein docking [3], and physics-based coarse-grained models with transferable potentials independent of any structural information to study the dynamics and aggregation of intrinsically disordered proteins.