Table 1.

Results of Monte Carlo simulation of the evolution protocols

Evolution method	Starting energy	Evolved energy	Achieved binding constant
Amino acid substitution	−17.00	−23.18	1
DNA shuffling	−17.00	−23.83	100
Swapping	0	−24.52	1.47  ×  104
Mixing	0	−24.88	1.81  ×  105
Multipool swapping	0	−25.40*	8.80  ×  106*

The starting polypeptide energy of −17.00 comes from a protein-like sequence (minimized U^sd), and 0 comes from a random initial sequence of amino acids. The evolved energies and binding constants are median values. The binding constants are calculated as ae^−bU, where a and b are constants determined by normalizing the binding constants achieved by point mutation and shuffling to 1 and 100, respectively. 

^*Note that the energies and binding constants achieved by means of multipool swapping represent typical best-evolved protein folds.