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. 2017 Dec 27;13(12):e1005905. doi: 10.1371/journal.pcbi.1005905

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© 2017 Alam et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 3 — 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).