High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
Fig 4
PIPER-FlexPepDock peptide docking performance.
(A) Overall performance on a non-redundant set of 27 peptide-protein complexes. Top: Distribution of best model L-RMSDs (among top 10 ranking clusters) for runs using the bound (BOUND) and free (UNBOUND & UNBOUND-MIN) receptor structures, the latter including also receptor flexibility in the final refinement step (only the motif region was modeled for the 12 complexes with known motif). Shown are both the L-RMSD values for each protein-peptide complex (grey circles, rounded values for improved visibility are provided), as well as the distribution (quartiles and medians, with median values printed alongside). Bottom: Distribution of the ranks of the first near-native cluster (defined as L-RMSD < = 2.0Å), shown using different shades (for corresponding results among the top1, top3 and top10 ranked predictions). (B) Comparison to performance by other algorithms. Top: Box plots of best L-RMSDs among top 10 ranking clusters, including results for the motif part where the motif is known (as in A), as well as for the full peptide, for comparison. Bottom: Performance is shown for different cutoffs (3.0Å and 2.0Å L-RMSD in left and right boxes, respectively) (See S1B Table for more details).