MOTIVATION 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 the protein'...

Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings,...

Various mechanisms can lead to the entrapment of air pockets within stormwater storage tunnels when they undergo rapid filling during intense rain events [Vasconcelos and Wright(2006)]. These entrapped air pockets are linked to operational issues within systems such as damaging surges, storage capacity loss, and severe geysering upon their release through water-filled ventilation shafts. Theref...

Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structurebased ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, ...

Many biological activities originate from interactions between small-molecule ligands and their protein targets. A detailed structural and physico-chemical characterization of these interactions could significantly deepen our understanding of protein function and facilitate drug design. Here, we present a large-scale study on a non-redundant set of about 20,000 known ligand-binding sites, or po...