Fig. 1: Overview of the FoldArchitect and RosettaScripts integration.
From: Sampling of structure and sequence space of small protein folds
a The FoldArchitect accepts user specification, which includes length ranges of secondary structure (SS) and loops, as well as how the distance constraints are applied (for instance, harmonic constraints). In addition, register shifts and beta bulges can be specified to introduce larger curvature into beta sheets. We then use the previously reported fragment insertion protocol1 and filter for geometrically realistic backbone conformations before designing the sequence of the new construct. After sequence design, the decoys are screened for their stability using varying concentrations of trypsin and chymotrypsin. The information gained from the stable designs was fed back into the FoldArchitect. b Various distance constraints (yellow lines) and secondary structure element pairing can be encoded in a fold-description file (following an XML format); the XML allows the user to specify next-to-length variations also, specific or ambiguous distance constraints, also pairing of helices or helix-sheet-helix, sheet orientations or bulge insertions into beta-sheets. c Polypeptide ABEGO regions within the Ramachandran plot can be specified for loop connections within RosettaScripts. Source data is provided as Source Data File.
