Conversion is done using only the twenty common naturally occurring amino acids in proteins, extendable to include other types of amino acids. The long term goal is to be able to perform de novo simulations to produce a potential three-dimensional structure of the string, and to find matching motifs for the string that exist in naturally occurring proteins (with and without known structure).
The applications of this are novelty (your name using the protein alphabet), as a teaching aid (to raise the interest of young people in protein structure -- for example, this was used as part of an interactive exhibit at the Paws-on-Science 2010 exhibit at the Seattle Pacific Science Center), and also for protein design.