Two-dimensional depiction of the pocket detection process of SURFNET. A: An initial gap sphere (blue disc) is placed midway between the van der Waals surfaces of a pair of atoms. The radius of this gap sphere is then reduced until it is not penetrated by any of the neighboring atoms. The resulting final gap sphere is shown in red. B: The arrangement of final gap spheres is used to describe the shapes and sizes of protein cavities in SURFNET.