Coarse-graining the potential energy surface into the basins of attraction of local minima, provides a computational framework for investigating structure, dynamics and thermodynamics in molecular science. Steps between local minima form the basis for global optimisation via basin-hopping and for calculating thermodynamic properties using the superposition approach and basin-sampling. To treat global dynamics we must include transition states of the potential energy surface, which link local minima via steepest-descent paths. We may then apply the discrete path sampling method, which provides access to rate constants for rare events. In large systems the paths between minima with unrelated structures may involve hundreds of stationary points of the potential energy surface. New algorithms have been developed for both geometry optimisation and making connections between distant local minima, which allow us to treat such systems. Applications will be presented for a wide variety of atomic and molecular clusters, glass-formers and biomolecules. Results for folding, misfolding and aggregation of peptides and proteins illustrate how experimental time and length scales can now be addressed for such systems.