RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Abstract

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins.

Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth

“…Consistent with the WT PG9 structure, antibody position 100 F is located on an antiparallel β-sheet at the apical mental Video 1). Next, we used RosettaDesign for a complete redesign of the HCDR sequence by simultaneously optimizing predicted thermodynamic stability of the antibody/HIV Env complex as well as predicted binding affinity (7)(8)(9)(10). RosettaDesign works by fixing the conformation of the backbone coordinates and optimizing the side-chains and amino acid identities to minimize the Rosetta energy function.…”

Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling

“…Computational design and docking were performed using Rosetta (19)(20)(21). A computationally guided ubiquitin library was displayed on the surface of M13 bacteriophage as previously described (22) and selected against the monobiotinylated catalytic domain of USP14 (residues D91-Q494, C114A active site mutation).…”

“…To explore the conformation and dynamics of ubiquitin's β1-β2 loop, we computationally searched for core positions where mutations are predicted to favor the USP-binding state, using both single-state and multistate RosettaDesign (Methods) (19)(20)(21)(22). Both types of design experiments identified a consistent set of positions for mutation ( Fig.…”

Computational design of a pH-sensitive IgG binding protein

“…We then searched for protein scaffolds with high bacterial expression and solubility that could host the hotspot residues in the correct relative orientations. After successful placement of the hotspot residues (Methods), the remainder of the interface was redesigned by using RosettaDesign (15,16) and designs were filtered and ranked based on computed binding energy and shape complementarity (Methods).…”

“…In parallel, 865 native scaffolds (11) were docked against Fc by PatchDock (22) constrained to bury Ile253, Met252, Met428, or Tyr436 using the "knob" feature. For each of the top 100 docked conformations, the capability to hold the hotspot residues as in the hotspot libraries was assessed similarly as previously described by using RosettaScripts (11,13,16) protocols Fc-2stubs.xml and Fc-3stubs.xml (SI Appendix). Three sets of hotspots were considered: a two-hotspot solution with Gln/Asn and Phe/Trp, and three-hotspot solution with Gln/Asn, Phe/Trp, and Leu disembodied residue libraries.…”