Fig. 7. Enhanced performance of rotamer recovery using flexible backbone modeling.

In panel A, the original backbone is shown in orange ribbons. The side chain conformations in the crystal structure of 1YN3 are shown in green. Side chain prediction with the repackSideChains program produced the conformations of four core residues displayed in magenta. In the model, the χ1 of Y₂₁₇ assumes a g− conformation instead of the g+ conformation that is observed in the crystal structure. Concurrently there is also a rearrangement of other three nearby positions to non-native rotamers. After the backbone has been locally relaxed with the Backrub algorithm (panel B, in blue) the lowest energy model recovers the native conformation.