The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: CORE_CONCEPTS SYMMETRY STRUCTURE_PREDICTION DESIGN DOCKING COMPARATIVE_MODELING
Frank Dimaio and Ingemar André dimaio@u.washington.edu and ingemar.andre@biochemistry.lu.se
Update: 2016-22-06 Sebastian Rämisch raemisch@scripps.edu
Examples of how to run symmetry-enabled rosetta protocols.
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 complex symmetries 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.
Rosetta can be downloaded at http://www.rosettacommons.org/software
The applications that are exemplified are fully documented in the regular Rosetta documentation. For a general description see:
Symmetry User Guide
Documentation for symmetric docking Documentation for fold-and-dock Documentation for fixed backbone design Documentation for comparative modeling Documentation for symmetry definitions
There is a more detailed tutorial in demos/public, called symmetric_docking_insulin_trimer_of_dimers
Defininately, take a look at that to understand how to do symmeric modeling in Rosetta.
(where ROSETTA3=path-to-Rosetta/main/source)
$> $ROSETTA3/bin/minirosetta.default.linuxgccrelease @comparative_modeling/input_files/comparative_modeling-flags$> $ROSETTA3/bin/fixbb.default.linuxgccrelease @fixbb/input_files/fixbb-symmetry-flags$> $ROSETTA3/bin/minirosetta.default.linuxgccrelease @fold-and-dock/input_files/fold-and-dock-flags$> $ROSETTA3/bin/SymDock.default.linuxgccrelease @symmetric_docking/input_files/symmetric-docking-flags