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PLoS One. 2011;6(6):e20450. doi: 10.1371/journal.pone.0020450. Epub 2011 Jun 22.

Modeling symmetric macromolecular structures in Rosetta3.

Author information

1
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America. dimaio@u.washington.edu

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.

PMID:
21731614
PMCID:
PMC3120754
DOI:
10.1371/journal.pone.0020450
[Indexed for MEDLINE]
Free PMC Article

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