Investigation of protein similarity using the Kolmogrov-Smirnov test

The near completion of the sequencing of the human and other genomes has provided a wealth of information that is yet to be interpreted. Similarity studies of proteins can often provide insights into protein function, as functionally similar proteins are often similar at some level of their primary, secondary, tertiary or quaternary organization. We propose the Kolmogorov-Smirnov statistic as a metric of protein similarity and demonstrate its use by comparing functionally related and unrelated proteins.