The pipeline for detection of cavity samples. a) A set of random samples is seeded in the space delimited by the radius 2R from the van der Waals spheres (yellow circles). b) Generation of sample points for two atoms. Note that more sample points are obtained in the intersection of both enlarged spheres. c) The samples p that lie inside the molecule (f(p) ≥ 0), are excluded. d) Detection of cavity samples is performed by means of shooting the ray (blue) along the gradient direction evaluated at all the samples. Those samples that hit the iso-surface (red) are labeled as potential cavity samples. Here only the rays that hit the iso-surface are rendered. e) The new sample position is computed, which is defined as the middle point between two points obtained by ray iso-surface intersection. f) The resulting graph components after the application of connected component and minimum spanning tree analysis.
Parulek et al. BMC Bioinformatics 2013 14(Suppl 19):S4 doi:10.1186/1471-2105-14-S19-S4