Understanding channel structures that lead to active sites or traverse a biomolecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Such studies require efficient methods for extracting, storing, and analyzing protein channels. Representing the structure of a biomolecule requires modeling its geometry and connectivity (topology). In this talk, I will discuss efficient representations of channels based on the alpha complex, methods to compute significant channels in biomolecules, and techniques for interactive visualization and exploration. These methods are implemented in a freely-available web server ChExVis. http://vgl.csa.iisc.ac.in/chexvis