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Figure 3
Contact restraint-guided ab initio models extend the tractable target range of AMPLE. Molecular-replacement (MR) success mapped against target chain length and median template-modelling score (TM-score). The point shape corresponds to the fold class of the target: all-α (circles), all-β (triangles) and mixed αβ (squares). The point colour indicates successful structure solutions for the contact constraints used: none (blue), PconsC2-only (red) and PconsC2+bbcontacts (gold). Points for successful solutions were considered in the order of Rosetta, PconsC2-only and PconsC2+bbcontacts decoys. In cases of unsuccessful molecular-replacement attempts (empty symbols), TM-scores for the largest clusters of PconsC2+bbcontacts decoys are shown. Median TM-scores for each point correspond to the largest decoy cluster (compared with the crystal structure), leading to a structure solution (cluster indices given next to each point for targets that were not solved with the largest cluster). The dashed grey line highlights the tested target chain-length limit of AMPLE (120 residues) for globular proteins (Bibby et al., 2012BB4). Cartoon representations of crystal structures of five different targets exemplify the diversity of structure solutions (PDB identifiers are provided next to each crystal structure). α-Helices are shown in red, β-sheets in yellow and loops in green.

Volume 3| Part 4| July 2016| Pages 259-270
ISSN: 2052-2525