The discovery of a new protein and its function was once
deemed worthy of a paper in its own right. Now with the
automation of the processes involved with the discovery
of new proteins it is almost viewed as common place.
Due to the large amount of new proteins being
discovered, automated processes are also needed to find what purpose a protein might have within a biological
system. This paper deals with the hierarchical functional
classification of enzymes (a sub set of proteins).
Enzymes are nature's catalysts and usually are more
effective at catalysing reactions than their non-biological
counterparts. An example of such effective enzymes are
those found in biological washing powder.
assigned EC codes (enzyme commission numbers), which
are 4 digit numbers that represent the type of chemical
reaction the enzyme in question catalyses [6]. Each digit
corresponds to a level in the hierarchy. For instance, EC
3.1.4.1 is an enzyme with class value 3 in the first level,
class value 1 in the second level, etc.
Proteins are formed from a number of amino acids chained
together. There are 20 different amino acids that occur
naturally, and a linear sequence of these amino acids is
known as the primary structure. The secondary structures
seen in proteins are the 3D shapes that form locally in each
protein and may be repeated throughout it. They also may be
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