Proteins are linear, unbranched polymers of the 20 naturally
occurring amino acid residues. Under physiological conditions,
most proteins self-assemble into a unique, biologically relevant
structure: the native fold. This structure can be dissected into
chemically recognizable, topologically simple elements of
secondary structure: a-helix, 310-helix, b-strand, polyproline
II helix, turns, and V-loops. Together, these six familiar motifs
account for ,95% of the total protein structure, and they are
utilized repeatedly in mix-and-match patterns, giving rise to the
repertoire of known folds. In principle, a protein’s threedimensional
structure is predictable from its amino acid
sequence, but this problem remains unsolved. A related, but
ostensibly simpler, problem is to predict a protein’s secondary
structure elements from its sequence.