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

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

doi:10.1371/journal.pone.0020161

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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	e20161
Journal	PLoS ONE
Volume	6
Issue number	6
DOIs	https://doi.org/10.1371/journal.pone.0020161
State	Published - Jun 2011
Externally published	Yes

All Science Journal Classification (ASJC) codes

General Biochemistry,Genetics and Molecular Biology
General Agricultural and Biological Sciences
General

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10.1371/journal.pone.0020161License: CC BY

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@article{b7529b40dc1a498dba04d4eae357010f,

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.",

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

note = "RosettaScripts is a collaborative project with contributions from the entire Rosetta community. We thank the many people who have contributed protocols, insights, and usage reports. Author Contributions Conceived and designed the experiments: SJF ALF JEC EMS SDK NK JA PM FR GL DB JM. Performed the experiments: SJF ALF JEC EMS SDK NK JA PM FR GL. Analyzed the data: SJF ALF JEC EMS SDK NK JA PM FR GL DB. Contributed reagents/materials/analysis tools: SJF ALF JEC EMS SDK NK JA PM FR GL. Wrote the paper: SJF ALF JEC EMS SDK NK JA PM FR GL DB. Funding: Funding was provided by the Howard Hughes Medical Institute, Defense Advanced Research Agency, and Defense Threat Reduction Agency. SJF was supported by a long-term fellowship from the Human Frontier Science Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.",

year = "2011",

month = jun,

doi = "10.1371/journal.pone.0020161",

language = "الإنجليزيّة",

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T2 - A scripting language interface to the Rosetta Macromolecular modeling suite

AU - Fleishman, Sarel J.

AU - Leaver-Fay, Andrew

AU - Corn, Jacob E.

AU - Strauch, Eva Maria

AU - Khare, Sagar D.

AU - Koga, Nobuyasu

AU - Ashworth, Justin

AU - Murphy, Paul

AU - Richter, Florian

AU - Lemmon, Gordon

AU - Meiler, Jens

AU - Baker, David

N1 - RosettaScripts is a collaborative project with contributions from the entire Rosetta community. We thank the many people who have contributed protocols, insights, and usage reports. Author Contributions Conceived and designed the experiments: SJF ALF JEC EMS SDK NK JA PM FR GL DB JM. Performed the experiments: SJF ALF JEC EMS SDK NK JA PM FR GL. Analyzed the data: SJF ALF JEC EMS SDK NK JA PM FR GL DB. Contributed reagents/materials/analysis tools: SJF ALF JEC EMS SDK NK JA PM FR GL. Wrote the paper: SJF ALF JEC EMS SDK NK JA PM FR GL DB. Funding: Funding was provided by the Howard Hughes Medical Institute, Defense Advanced Research Agency, and Defense Threat Reduction Agency. SJF was supported by a long-term fellowship from the Human Frontier Science Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

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