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

2011; Public Library of Science; Volume: 6; Issue: 6 Linguagem: Inglês

10.1371/journal.pone.0020161

1932-6203

Sarel J. Fleishman, Andrew Leaver‐Fay, Jacob E. Corn, Eva‐Maria Strauch, Sagar D. Khare, Nobuyasu Koga, J. R. Ashworth, Paul Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, David Baker,

Microbial Metabolic Engineering and Bioproduction

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.