CavVisA Field-of-View Geometric Algorithm for Protein Cavity Detection

Several
geometric-based methods have been developed for the last
two to three decades to detect and identify cavities (i.e., putative
binding sites) on proteins, as needed to study protein–ligand
interactions and protein docking. This paper introduces a new protein
cavity method, called CavVis, which combines voxelization (i.e., a
grid of voxels) and an analytic formulation of Gaussian surfaces that
approximates the solvent-excluded surface. This method builds upon
visibility of points on protein surface to find its cavities. Specifically,
the visibility criterion combines three concepts we borrow from computer
graphics, the field-of-view of each surface point, voxel ray casting,
and back-face culling.