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Anchored Design of Protein-Protein Interfaces

Figure 3. Protocol flowchart. This flowchart summarizes the AnchoredDesign protocol and process. In the top part, preliminary steps are marked
in green. These steps are primarily manual but can be assisted with AnchorFinder and AnchoredPDBCreator. Initial steps vary depending on whether
the benchmarking case for this paper, or the more general design case, is being addressed. The steps of the AnchoredDesign protocol are shown in
blue and pink. The perturbation steps, performed in centroid mode, are in blue. The refinement steps, performed with a fully atomic representation,
are in pink. In both portions of the protocol, many Monte Carlo cycles are performed; the results here used 500 perturb and 1000 refine cycles, but
optimal cycle counts are best determined on a per-experiment basis.
doi:10.1371/journal.pone.0020872.g003

PLoS ONE | www.plosone.org 4 June 2011 | Volume 6 | Issue 6 | e20872