Modeling Symmetric Macromolecular Structures in Rosetta3
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/2032564
- author
- DiMaio, Frank ; Leaver-Fay, Andrew ; Bradley, Phil ; Baker, David and André, Ingemar LU
- organization
- publishing date
- 2011
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 6
- issue
- 6
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- wos:000292033700008
- scopus:79959458821
- pmid:21731614
- 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
- 2016-04-01 13:01:55
- date last changed
- 2022-03-29 05:06:29
@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 (PLoS)}}, series = {{PLoS ONE}}, title = {{Modeling Symmetric Macromolecular Structures in Rosetta3}}, url = {{http://dx.doi.org/10.1371/journal.pone.0020450}}, doi = {{10.1371/journal.pone.0020450}}, volume = {{6}}, year = {{2011}}, }