Rosettascripts: A scripting language interface to the Rosetta Macromolecular modeling suite

Fleishman, SJ; Leaver-Fay, A; Corn, JE; Strauch, EM; Khare, SD; Koga, N; Ashworth, J; Murphy, P; Richter, F; Lemmon, G; Meiler, J; Baker, D

Rosettascripts: A scripting language interface to the Rosetta Macromolecular modeling suite

Fleishman, SJ Leaver-Fay, A Corn, JE Strauch, EM Khare, SD Koga, N Ashworth, J

Murphy, P Richter, F Lemmon, G Meiler, J Baker, D

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Publication Type:: Journal Article
Citation:: PLoS ONE, 2011, 6 (6)
Issue Date:: 2011-06-30

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Field	Value	Language
dc.contributor.author	Fleishman, SJ	en_US
dc.contributor.author	Leaver-Fay, A	en_US
dc.contributor.author	Corn, JE	en_US
dc.contributor.author	Strauch, EM	en_US
dc.contributor.author	Khare, SD	en_US
dc.contributor.author	Koga, N	en_US
dc.contributor.author	Ashworth, J https://orcid.org/0000-0003-4835-6551	en_US
dc.contributor.author	Murphy, P	en_US
dc.contributor.author	Richter, F	en_US
dc.contributor.author	Lemmon, G	en_US
dc.contributor.author	Meiler, J	en_US
dc.contributor.author	Baker, D	en_US
dc.date.available	2011-04-12	en_US
dc.date.issued	2011-06-30	en_US
dc.identifier.citation	PLoS ONE, 2011, 6 (6)	en_US
dc.identifier.uri	http://hdl.handle.net/10453/116425
dc.description.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. © 2011 Fleishman et al.	en_US
dc.relation.ispartof	PLoS ONE	en_US
dc.relation.isbasedon	10.1371/journal.pone.0020161	en_US
dc.subject.classification	General Science & Technology	en_US
dc.subject.mesh	DNA-Binding Proteins	en_US
dc.subject.mesh	Ligands	en_US
dc.subject.mesh	Protein Conformation	en_US
dc.subject.mesh	Models, Molecular	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Programming Languages	en_US
dc.subject.mesh	User-Computer Interface	en_US
dc.title	Rosettascripts: A scripting language interface to the Rosetta Macromolecular modeling suite	en_US
dc.type	Journal Article
utslib.citation.volume	6	en_US
utslib.for	MD Multidisciplinary	en_US
utslib.for	080301 Bioinformatics Software	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.issue	6	en_US
pubs.publication-status	Published	en_US
pubs.volume	6	en_US

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. © 2011 Fleishman et al.

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http://hdl.handle.net/10453/116425