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

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

in Algorithms / Amino acids / Binding proteins / Biochemistry / Biology / Biotechnology / Catalysis / Computer applications / Deoxyribonucleic acid / Design / DNA / DNA-binding protein / DNA-Binding Proteins - chemistry / Docking / Enzymes / Flexibility / Language / Ligands / Macromolecules / Models, Molecular / Programming Languages / Protein binding / Protein Conformation / Proteins / Protocol / Redesign / Robotics / Software / User-Computer Interface

2011

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

2011

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

2011

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Journal Article

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

Fleishman, Sarel J.,

Strauch, Eva-Maria,

Murphy, Paul,

Baker, David,

Corn, Jacob E.,

Meiler, Jens,

Lemmon, Gordon,

Leaver-Fay, Andrew,

Ashworth, Justin,

Richter, Florian,

Koga, Nobuyasu,

Khare, Sagar D.

2011

Overview

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.

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Publisher

Public Library of Science,Public Library of Science (PLoS)

Subject

/ Biology