Rosetta Documentation

Rosetta user guides are available from our online archive.

The user guide for the latest release is Rosetta 3.1 User Guide.

Additional Rosetta Software documentation and support are available at the RosettaCommons Tiki.

Documentation and support for PyRosetta are available through http://pyrosetta.org/.


One of the Ran's binding partners 1A2K.pdb which was predicted by the design simulations. (Humphris EL, Kortemme T., PLoS Comput Biol. 2007 Aug;3(8):e164. Epub 2007 Jul 5.)

New features of the current release (Rosetta 3.1)

Enzyme Design: This application takes an input structure containing one ligand/substrate in contact with a protein and repacks or redesigns the protein around it. Optionally, special catalytic contacts between ligand and protein can be specified, and this application can be used to optimize them.

Symmetry enforcement: The symmetry code in Rosetta was developed to provide a framework to enforce symmetry in the conformation among equivalent subunits in the assembly.

Membrane protein prediction: This protocol was developed to predict structures of helical membrane proteins with and without experimental constraints.

ddG prediction: This application estimates the impact of a sequence change on a protein's stability. It can perform single mutations as well as multiple mutations.

Kinematic Loop Modeling: Kinematic closure (KIC) is a modeling technique inspired by inverse-kinematics from robotics. KIC modes use exact kinematic closure for loop buiding and/or refinement, and will not introduce chainbreaks. Fragment files are not required/used in KIC modes.

RosettaScripts: RosettaScripts now computes alanine-scanning and other energy statistics for protein interfaces and carries out loop remodeling, design and docking in a user-friendly xml-based interface.

Scenarios - minor applications targeted at specific problems

  • FloppyTail: This code was intended to model the reach of a long flexible tail and determine whether a hypothesized binding site for the tail was plausible.
  • Loops-from-Density: This is a simple routine aimed at creating loopfiles for remodelling structures into density.
  • CA-to-allatom: This is an application intended to aid in building a full-atom model from a low-resolution C-alpha-only trace (such as hand-traced models from cryo-electron microscopy).