On quantification of geometry and topology of protein pockets and channels for assessing mutation effects

Geometric and topological features of proteins such as voids, pockets and channels are important for protein functions. We discuss a method for visualizing protein pockets and channels based on orthogonal spheres computed from alpha shapes of the protein structures, and how metric properties of channel surfaces can be mapped. In addition, we discuss how structurally prominent sites, such as constriction sties in channels, can be computed, which may help to understand protein functions and mutation effects, with implications in developing novel therapeutic interventions.