High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
Fig 3
Examples of global peptide docking energy landscapes.
Left: PDB id 1CZY (coiled peptide); Center: 1JD5 (extended peptide); Right: 2A3I (helical peptide). (A) Energy landscape as sampled in the first docking step of the protocol by PIPER rigid body docking of peptide fragments onto the unbound receptor structure. (B-D) Energy landscapes for the PIPER-FPD scheme, starting from the unbound receptor structure (B), the unbound receptor structure including receptor flexibility (C), and the corresponding bound receptor for comparison (D). Models are colored according to fragment quality, as in previous Figures. (E) Comparison of the modeled to the native structure (shown in blue and green, respectively).