Figure 1.

Differences between alternative structure log occupancies in parental and recombinant proteins. The average differences after one million generations for eight high-, 24 medium-, and 32 low-designable target (native) structures are represented with squares, triangles and circles, respectively, with results for each structure replicated four times. The differences in the natural log occupancies decrease linearly with the number of shared contact pairs, although there are many fewer alternative structures with large rather than small numbers of shared contacts -- and thus much more variable results. The difference in log occupancies between low-designable and medium- and high-designable structures is consistent, meaning that the occupancy of alternative (non-native) folds in low-designable recombinants is about one- to two-fold higher.