The scripts and input files that accompany this demo can be found in the
demos/protocol_captures directory of the Rosetta weekly releases.
This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.
KEYWORDS: STRUCTURE_PREDICTION SYMMETRY
Frank Dimaio and Ingemar André
dimaio@u.washington.edu and ingemar.andre@biochemistry.lu.se
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 www.rosettacommons.org/software
The applications that are exemplified are fully documented in the regular Rosetta documentation. For a general description see http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/.
Documentation for symmetric docking: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/symmetric_docking.html Documentation for fold-and-dock: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/fold_and_dock.html Documentation for fixed backbone design: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/fixed_backbone.html Documentation for comparative modeling: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/comparative_modeling.html