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Modeling Symmetric Macromolecular Structures in Rosetta3

DiMaio, Frank; Leaver-Fay, Andrew; Bradley, Phil; Baker, David and André, Ingemar LU (2011) In PLoS ONE 6(6).
Abstract
Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design... (More)
Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
PLoS ONE
volume
6
issue
6
publisher
Public Library of Science
external identifiers
  • wos:000292033700008
  • scopus:79959458821
ISSN
1932-6203
DOI
10.1371/journal.pone.0020450
language
English
LU publication?
yes
id
24ed7365-fc99-4b38-ad76-00745644ac01 (old id 2032564)
date added to LUP
2011-07-26 14:17:42
date last changed
2017-11-12 03:34:29
@article{24ed7365-fc99-4b38-ad76-00745644ac01,
  abstract     = {Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems.},
  author       = {DiMaio, Frank and Leaver-Fay, Andrew and Bradley, Phil and Baker, David and André, Ingemar},
  issn         = {1932-6203},
  language     = {eng},
  number       = {6},
  publisher    = {Public Library of Science},
  series       = {PLoS ONE},
  title        = {Modeling Symmetric Macromolecular Structures in Rosetta3},
  url          = {http://dx.doi.org/10.1371/journal.pone.0020450},
  volume       = {6},
  year         = {2011},
}