Abstract: Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling problem remains to be a grand challenge in computational analysis of relevant processes. Here we propose and demonstrate an entropy estimation method that is based on physical partition of configurational space and can be readily combined with currently available methodologies. Tests with two globular proteins suggest that for flexible macromolecules with large and complex configurational space, accurate configurational entropy estimation may be achieved simply by considering the entropically most important subspace, thus convert an exhaustive sampling problem into a local sampling problem.