Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.
Proteases are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a covalent intermediate with the protein to be cleaved; in the second step, water comes in and releases the second half of the cleaved protein.
Serine proteases include a number of digestive enzymes, including Trypsin, Chymotrypsin, and Elastase.
article describing Jmol [1] to the rescue.