A two amino acid (hydrophobic and polar) scheme is used to perform the
design on target conformations corresponding to the native states of 20
single chain proteins, Strikingly, the percentage of successful
identification of the nature of the residues benchmarked against
naturally occurring proteins and their homologues is around 75%,
independent of the complexity of the design procedure. Typically the
lowest success rate occurs for residues such as alanine that have a high
secondary structure functionality. Using a simple lattice model, we
argue that one possible shortcoming of the model studied may involve the
coarse-graining of the 20 kinds of amino acids into just two effective
types.
