Figure 2.

Illustrations of the native topomers for the proteins 1aps, 1ci2, 1urn, and 1lmb. Shown are the top 25 conformations (red) selected by a simple clustering procedure on the full l_c=12, r_c=8 Å topomer ensembles. Each of the 25 conformations is optimally superimposed on the corresponding native structure (dark trace). In the clustering procedure, the highest ranking conformation is the one with the largest number of conformational neighbors, where two conformations are considered to be neighbors if their rmsd is less than a certain cutoff (1.3–4.0 Å). The next highest ranking conformation is the conformation with most neighbors in the reduced ensemble, where the highest-ranking conformation and its neighbors have been excluded, and so on.