title: 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.
authors: Department of Biochemistry, University of Washington, Seattle, Washington, United States of America. sarelf@uw.edu
authors: Sarel J
authors: SJ
authors: Fleishman
authors: Andrew
authors: A
authors: Leaver-Fay
authors: Jacob E
authors: JE
authors: Corn
authors: Eva-Maria
authors: EM
authors: Strauch
authors: Sagar D
authors: SD
authors: Khare
authors: Nobuyasu
authors: N
authors: Koga
authors: Justin
authors: J
authors: Ashworth
authors: Paul
authors: P
authors: Murphy
authors: Florian
authors: F
authors: Richter
authors: Gordon
authors: G
authors: Lemmon
authors: Jens
authors: J
authors: Meiler
authors: David
authors: D
authors: Baker
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D011381:Programming Languages; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
chemical_list: D004268:DNA-Binding Proteins; D008024:Ligands