Figure 3

Quality of our rotamer library. We study the extent to which our set of rotamers can approximate the bound side-chains for our data set of 700 patches. For each patch we graft the bound side-chains onto the unbound backbone (bound_UBB conformation) and make an alternate graft of the closest rotamers in our rotamer library (rotamer_UBB conformation). The all-atom RMSDs between these grafts provide evidence that our rotamer library is extensive enough to produce a side-chain configuration near the bound. In all but 24 of the 700 patches this RMSD (blue, left bar) is within 1 Å. When we account for the changes in the backbone conformation between the bound and unbound conformations of the patch however, results are not as good. The maroon (center) and yellow (right) bars show the all-atom RMSD between the bound conformation of the patch and the bound_UBB and rotamer_UBB conformations, respectively. In 185 of the 700 patches, the rotamer_UBB conformation is more than 1 Å away from the bound conformation of the patch.