title: Modeling symmetric macromolecular structures in Rosetta3.
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.
authors: Department of Biochemistry, University of Washington, Seattle, Washington, United States of America. dimaio@u.washington.edu
authors: Frank
authors: F
authors: DiMaio
authors: Andrew
authors: A
authors: Leaver-Fay
authors: Phil
authors: P
authors: Bradley
authors: David
authors: D
authors: Baker
authors: Ingemar
authors: I
authors: André
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D040681:Structural Homology, Protein; D013816:Thermodynamics
chemical_list: D046911:Macromolecular Substances; D011506:Proteins