Proteins: Structure, Function and Genetics 32, 80-87, (1998).
Design of Proteins With Hydrophobic and Polar Amino Acids
Cristian Micheletti, Flavio Seno, Amos Maritan and Jayanth R. Banavar
Link to online article.
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.