What makes for a good folding? In proteins the usual measure is
the Gibbs free energy, a thermodynamic quantity that depends on
both energy and entropy. If you could tug on the ends of a
protein chain and straighten it out, the result would be a state
of high energy and low entropy. The energy is high because amino
acids that "want" to be close together are held at a distance;
the entropy is low because the straight chain is a highly
ordered configuration. When you let go, the chain springs back
into a shape with lower energy and higher entropy, changes that
translate into a lower value of the Gibbs free energy. The
"native" state of a protein—the folding it adopts under natural
conditions—is usually assumed to be the state with the lowest
possible free energy. Prototeins can get along with a simpler
folding criterion. Standard practice is to rank foldings simply
by counting H-H contacts. It's more like keeping score than
measuring energy. If the H's are viewed as analogues of
hydrophobic amino acids, the sco