Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes, or “pockets”, on protein surface. CAVITATOR is a program developed to detect “pocket” or “cavity” in a protein structure, using a grid-based geometric analysis. Details of Cavitator can be found in the following references:
Mu Gao and Jeffrey Skolnick, 2013, APoc: large-scale identification of similar protein pockets. Bioinformatics, 29(5):597-604. PDF
This software is freely available to ALL users.