Figure 5

Reducing sample size of test patches with SCMF. All-atom RMSD between the unbound conformation (green dot), the best pick in the SCMF-filtered ensemble (red cross), the theoretical rotamer_UBB conformation (black diamond), and the bound state for all 700 patches in our data set. To improve clarity, these test cases are arranged along the x-axis in order of increasing RMSD between the unbound and bound conformations. For 521 of the 700 cases, the best pick is within 1 Å RMSD of the bound conformation. (Note that the unbound conformation is not yet added to ensemble). We observe that for some of the patches, the best pick is better than the rotamer_UBB conformation: this indicates that local arrangement of the side-chain does not always lead to a good conformation for the patch as a whole (see text for details).