Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity
Assessment of sampling efficiency for the 90 loops modeled in the CASP9 experiment (see Materials and Methods for selection). All loops were modeled with very limited number of templates, mostly 1–5, and with templates of various lengths. For smaller loops with 3–8 residues, global RMSD is mostly below 2.5 Å. For medium sized loops (8–13 amino acids), global RMSD is between 1–3 Å. As the loop length increases, best-sampled conformations have higher RMSD from the native structure. The DPM-HMM fails after 20 residues as shown by the increase in RMSD above 5 Å.